Target Binding Site Detail
Target General Information | Top | ||||
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Target ID | T30082 | Target Info | |||
Target Name | Acetylcholinesterase (AChE) | ||||
Synonyms | YT; N-ACHE; ARACHE | ||||
Target Type | Successful Target | ||||
Gene Name | ACHE | ||||
Biochemical Class | Carboxylic ester hydrolase | ||||
UniProt ID |
Ligand General Information | Top | ||||
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Ligand Name | 4-(Aminocarbonyl)-1-[({2-[(E)-(hydroxyimino)methyl]pyridinium-1-YL}methoxy)methyl]pyridinium | Ligand Info | |||
Canonical SMILES | C1=CC=[N+](C(=C1)C=NO)COC[N+]2=CC=C(C=C2)C(=O)N | ||||
InChI | 1S/C14H14N4O3/c15-14(19)12-4-7-17(8-5-12)10-21-11-18-6-2-1-3-13(18)9-16-20/h1-9H,10-11H2,(H-,15,19)/p+2 | ||||
InChIKey | FJZDLOMCEPUCII-UHFFFAOYSA-P | ||||
PubChem Compound ID | 135412778 |
Drug Binding Sites of Target | Top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PDB ID: 6WVO Crystal Structure of Recombinant Human Acetylcholinesterase In Complex with GD and HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPNDTEL 269 VACLRTRPAQ279 VLVNHEWHVL289 PQESVFRFSF299 VPVVDGDFLS309 DTPEALINAG 319 DFHGLQVLVG329 VVKDEGSYFL339 VYGAPGFSKD349 NESLISRAEF359 LAGVRVGVPQ 369 VSDLAAEAVV379 LHYTDWLHPE389 DPARLREALS399 DVVGDHNVVC409 PVAQLAGRLA 419 AQGARVYAYV429 FEHRASTLSW439 PLWMGVPHGY449 EIEFIFGIPL459 DPSRNYTAEE 469 KIFAQRLMRY479 WANFARTGDP489 NEPPKAPQWP501 PYTAGAQQYV511 SLDLRPLEVR 521 RGLRAQACAF531 WNRFLPKLLS541 A
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☰6WVO Nodes: OProtein ▢Nucleotide ◇Chemical ▢Biopolymer Lines: Interactions at 4 Å Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
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PDB ID: 5HF9 Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [2] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPNDTEL 269 VACLRTRPAQ279 VLVNHEWHVL289 PQESVFRFSF299 VPVVDGDFLS309 DTPEALINAG 319 DFHGLQVLVG329 VVKDEGSYFL339 VYGAPGFSKD349 NESLISRAEF359 LAGVRVGVPQ 369 VSDLAAEAVV379 LHYTDWLHPE389 DPARLREALS399 DVVGDHNVVC409 PVAQLAGRLA 419 AQGARVYAYV429 FEHRASTLSW439 PLWMGVPHGY449 EIEFIFGIPL459 DPSRNYTAEE 469 KIFAQRLMRY479 WANFARTGDP489 NEPRDPQWPP502 YTAGAQQYVS512 LDLRPLEVRR 522 GLRAQACAFW532 NRFLPKLLSA542
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☰5HF9 Nodes: OProtein ▢Nucleotide ◇Chemical ▢Biopolymer Lines: Interactions at 4 Å Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
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PDB ID: 6CQW Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with VX(-) and HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.28 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
REDAELLVTV
12 RGGRLRGIRL22 KTPGGPVSAF32 LGIPFAEPPM42 GPRRFLPPEP52 KQPWSGVVDA 62 TTFQSVCYQY72 VDTLYPGFEG82 TEMWNPNREL92 SEDCLYLNVW102 TPYPRPTSPT 112 PVLVWIYGGG122 FYSGASSLDV132 YDGRFLVQAE142 RTVLVSMNYR152 VGAFGFLALP 162 GSREAPGNVG172 LLDQRLALQW182 VQENVAAFGG192 DPTSVTLFGE202 SAGAASVGMH 212 LLSPPSRGLF222 HRAVLQSGAP232 NGPWATVGMG242 EARRRATQLA252 HLVGCPPGGN 265 DTELVACLRT275 RPAQVLVNHE285 WHVLPQESVF295 RFSFVPVVDG305 DFLSDTPEAL 315 INAGDFHGLQ325 VLVGVVKDEG335 SYFLVYGAPG345 FSKDNESLIS355 RAEFLAGVRV 365 GVPQVSDLAA375 EAVVLHYTDW385 LHPEDPARLR395 EALSDVVGDH405 NVVCPVAQLA 415 GRLAAQGARV425 YAYVFEHRAS435 TLSWPLWMGV445 PHGYEIEFIF455 GIPLDPSRNY 465 TAEEKIFAQR475 LMRYWANFAR485 TGDPNEPAPQ499 WPPYTAGAQQ509 YVSLDLRPLE 519 VRRGLRAQAC529 AFWNRFLPKL539 LSA
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☰6CQW Nodes: OProtein ▢Nucleotide ◇Chemical ▢Biopolymer Lines: Interactions at 4 Å Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
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PDB ID: 6CQU Crystal Structure of Recombinant Human Acetylcholinesterase with Reactivator HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.31 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
REDAELLVTV
12 RGGRLRGIRL22 KTPGGPVSAF32 LGIPFAEPPM42 GPRRFLPPEP52 KQPWSGVVDA 62 TTFQSVCYQY72 VDTLYPGFEG82 TEMWNPNREL92 SEDCLYLNVW102 TPYPRPTSPT 112 PVLVWIYGGG122 FYSGASSLDV132 YDGRFLVQAE142 RTVLVSMNYR152 VGAFGFLALP 162 GSREAPGNVG172 LLDQRLALQW182 VQENVAAFGG192 DPTSVTLFGE202 SAGAASVGMH 212 LLSPPSRGLF222 HRAVLQSGAP232 NGPWATVGMG242 EARRRATQLA252 HLVGCPPTGG 264 NDTELVACLR274 TRPAQVLVNH284 EWHVLPQESV294 FRFSFVPVVD304 GDFLSDTPEA 314 LINAGDFHGL324 QVLVGVVKDE334 GSYFLVYGAP344 GFSKDNESLI354 SRAEFLAGVR 364 VGVPQVSDLA374 AEAVVLHYTD384 WLHPEDPARL394 REALSDVVGD404 HNVVCPVAQL 414 AGRLAAQGAR424 VYAYVFEHRA434 STLSWPLWMG444 VPHGYEIEFI454 FGIPLDPSRN 464 YTAEEKIFAQ474 RLMRYWANFA484 RTGDPNEPQW500 PPYTAGAQQY510 VSLDLRPLEV 520 RRGLRAQACA530 FWNRFLPKLL540 SA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:73 or .A:74 or .A:87 or .A:124 or .A:125 or .A:282 or .A:283 or .A:285 or .A:286 or .A:337 or .A:338 or .A:341; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6WV1 Crystal Structure of Recombinant Human Acetylcholinesterase In Complex with GB and HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.37 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
REDAELLVTV
12 RGGRLRGIRL22 KTPGGPVSAF32 LGIPFAEPPM42 GPRRFLPPEP52 KQPWSGVVDA 62 TTFQSVCYQY72 VDTLYPGFEG82 TEMWNPNREL92 SEDCLYLNVW102 TPYPRPTSPT 112 PVLVWIYGGG122 FYSGASSLDV132 YDGRFLVQAE142 RTVLVSMNYR152 VGAFGFLALP 162 GSREAPGNVG172 LLDQRLALQW182 VQENVAAFGG192 DPTSVTLFGE202 SAGAASVGMH 212 LLSPPSRGLF222 HRAVLQSGAP232 NGPWATVGMG242 EARRRATQLA252 HLVGCPPGGN 265 DTELVACLRT275 RPAQVLVNHE285 WHVLPQESVF295 RFSFVPVVDG305 DFLSDTPEAL 315 INAGDFHGLQ325 VLVGVVKDEG335 SYFLVYGAPG345 FSKDNESLIS355 RAEFLAGVRV 365 GVPQVSDLAA375 EAVVLHYTDW385 LHPEDPARLR395 EALSDVVGDH405 NVVCPVAQLA 415 GRLAAQGARV425 YAYVFEHRAS435 TLSWPLWMGV445 PHGYEIEFIF455 GIPLDPSRNY 465 TAEEKIFAQR475 LMRYWANFAR485 TGDPNEPAPQ499 WPPYTAGAQQ509 YVSLDLRPLE 519 VRRGLRAQAC529 AFWNRFLPKL539 LSA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:74 or .A:124 or .A:282 or .A:283 or .A:285 or .A:286 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:337 or .A:338 or .A:341; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6CQY Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with EMPA and HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.45 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPPGGND 266 TELVACLRTR276 PAQVLVNHEW286 HVLPQESVFR296 FSFVPVVDGD306 FLSDTPEALI 316 NAGDFHGLQV326 LVGVVKDEGS336 YFLVYGAPGF346 SKDNESLISR356 AEFLAGVRVG 366 VPQVSDLAAE376 AVVLHYTDWL386 HPEDPARLRE396 ALSDVVGDHN406 VVCPVAQLAG 416 RLAAQGARVY426 AYVFEHRAST436 LSWPLWMGVP446 HGYEIEFIFG456 IPLDPSRNYT 466 AEEKIFAQRL476 MRYWANFART486 GDPNEPAPQW500 PPYTAGAQQY510 VSLDLRPLEV 520 RRGLRAQACA530 FWNRFLPKLL540 SA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:74 or .A:124 or .A:282 or .A:283 or .A:285 or .A:286 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:337 or .A:338 or .A:341; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6WUY Crystal Structure of Recombinant Human Acetylcholinesterase In Complex with GA and HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.46 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPPNDTE 268 LVACLRTRPA278 QVLVNHEWHV288 LPQESVFRFS298 FVPVVDGDFL308 SDTPEALINA 318 GDFHGLQVLV328 GVVKDEGSYF338 LVYGAPGFSK348 DNESLISRAE358 FLAGVRVGVP 368 QVSDLAAEAV378 VLHYTDWLHP388 EDPARLREAL398 SDVVGDHNVV408 CPVAQLAGRL 418 AAQGARVYAY428 VFEHRASTLS438 WPLWMGVPHG448 YEIEFIFGIP458 LDPSRNYTAE 468 EKIFAQRLMR478 YWANFARTGD488 PNEPAPQWPP502 YTAGAQQYVS512 LDLRPLEVRR 522 GLRAQACAFW532 NRFLPKLLSA542
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:74 or .A:87 or .A:124 or .A:125 or .A:285 or .A:286 or .A:289 or .A:296 or .A:297 or .A:298 or .A:337 or .A:338 or .A:341; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6NTM Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-232 in Complex with the Reactivator, HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPPGGND 266 TELVACLRTR276 PAQVLVNHEW286 HVLPQESVFR296 FSFVPVVDGD306 FLSDTPEALI 316 NAGDFHGLQV326 LVGVVKDEGS336 YFLVYGAPGF346 SKDNESLISR356 AEFLAGVRVG 366 VPQVSDLAAE376 AVVLHYTDWL386 HPEDPARLRE396 ALSDVVGDHN406 VVCPVAQLAG 416 RLAAQGARVY426 AYVFEHRAST436 LSWPLWMGVP446 HGYEIEFIFG456 IPLDPSRNYT 466 AEEKIFAQRL476 MRYWANFART486 GDPNEPAPQW500 PPYTAGAQQY510 VSLDLRPLEV 520 RRGLRAQACA530 FWNRFLPKLL540 SA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:73 or .A:74 or .A:87 or .A:124 or .A:125 or .A:282 or .A:283 or .A:285 or .A:286 or .A:337 or .A:338 or .A:341; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6CQV Crystal Structure of Recombinant Human Acetylcholinesterase in Complex with VX(+) and HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
REDAELLVTV
12 RGGRLRGIRL22 KTPGGPVSAF32 LGIPFAEPPM42 GPRRFLPPEP52 KQPWSGVVDA 62 TTFQSVCYQY72 VDTLYPGFEG82 TEMWNPNREL92 SEDCLYLNVW102 TPYPRPTSPT 112 PVLVWIYGGG122 FYSGASSLDV132 YDGRFLVQAE142 RTVLVSMNYR152 VGAFGFLALP 162 GSREAPGNVG172 LLDQRLALQW182 VQENVAAFGG192 DPTSVTLFGE202 SAGAASVGMH 212 LLSPPSRGLF222 HRAVLQSGAP232 NGPWATVGMG242 EARRRATQLA252 HLVGCPPTGG 264 NDTELVACLR274 TRPAQVLVNH284 EWHVLPESVF295 RFSFVPVVDG305 DFLSDTPEAL 315 INAGDFHGLQ325 VLVGVVKDEG335 SYFLVYGAPG345 FSKDNESLIS355 RAEFLAGVRV 365 GVPQVSDLAA375 EAVVLHYTDW385 LHPEDPARLR395 EALSDVVGDH405 NVVCPVAQLA 415 GRLAAQGARV425 YAYVFEHRAS435 TLSWPLWMGV445 PHGYEIEFIF455 GIPLDPSRNY 465 TAEEKIFAQR475 LMRYWANFAR485 TGDPNEAPQW500 PPYTAGAQQY510 VSLDLRPLEV 520 RRGLRAQACA530 FWNRFLPKLL540 SA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:74 or .A:75 or .A:86 or .A:120 or .A:121 or .A:124 or .A:125 or .A:133 or .A:202 or .A:337 or .A:341 or .A:447 or .A:448 or .A:449 or .A:451; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6NTG Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-234 in Complex with Reactivator, HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.65 Å | Mutation | No | [5] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPGNDTE 268 LVACLRTRPA278 QVLVNHEWHV288 LPQESVFRFS298 FVPVVDGDFL308 SDTPEALINA 318 GDFHGLQVLV328 GVVKDEGSYF338 LVYGAPGFSK348 DNESLISRAE358 FLAGVRVGVP 368 QVSDLAAEAV378 VLHYTDWLHP388 EDPARLREAL398 SDVVGDHNVV408 CPVAQLAGRL 418 AAQGARVYAY428 VFEHRASTLS438 WPLWMGVPHG448 YEIEFIFGIP458 LDPSRNYTAE 468 EKIFAQRLMR478 YWANFARTGD488 PNEPAPQWPP502 YTAGAQQYVS512 LDLRPLEVRR 522 GLRAQACAFW532 NRFLPKLLSA542
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:74 or .A:124 or .A:282 or .A:283 or .A:285 or .A:286 or .A:293 or .A:294 or .A:295 or .A:337 or .A:338 or .A:341; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PDB ID: 6NTN Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-230 in Complex with the Reactivator, HI-6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [6] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
EDAELLVTVR
13 GGRLRGIRLK23 TPGGPVSAFL33 GIPFAEPPMG43 PRRFLPPEPK53 QPWSGVVDAT 63 TFQSVCYQYV73 DTLYPGFEGT83 EMWNPNRELS93 EDCLYLNVWT103 PYPRPTSPTP 113 VLVWIYGGGF123 YSGASSLDVY133 DGRFLVQAER143 TVLVSMNYRV153 GAFGFLALPG 163 SREAPGNVGL173 LDQRLALQWV183 QENVAAFGGD193 PTSVTLFGES203 AGAASVGMHL 213 LSPPSRGLFH223 RAVLQSGAPN233 GPWATVGMGE243 ARRRATQLAH253 LVGCPPTGGN 265 DTELVACLRT275 RPAQVLVNHE285 WHVLPQESVF295 RFSFVPVVDG305 DFLSDTPEAL 315 INAGDFHGLQ325 VLVGVVKDEG335 SYFLVYGAPG345 FSKDNESLIS355 RAEFLAGVRV 365 GVPQVSDLAA375 EAVVLHYTDW385 LHPEDPARLR395 EALSDVVGDH405 NVVCPVAQLA 415 GRLAAQGARV425 YAYVFEHRAS435 TLSWPLWMGV445 PHGYEIEFIF455 GIPLDPSRNY 465 TAEEKIFAQR475 LMRYWANFAR485 TGDPNEPAPQ499 WPPYTAGAQQ509 YVSLDLRPLE 519 VRRGLRAQAC529 AFWNRFLPKL539 LSA
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HI6 or .HI62 or .HI63 or :3HI6;style chemicals stick;color identity;select .A:72 or .A:73 or .A:74 or .A:87 or .A:124 or .A:125 or .A:282 or .A:283 or .A:285 or .A:286 or .A:337 or .A:338 or .A:341; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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References | Top | ||||
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REF 1 | Structural and Biochemical Insights into the Inhibition of Human Acetylcholinesterase by G-Series Nerve Agents and Subsequent Reactivation by HI-6. Chem Res Toxicol. 2021 Mar 15;34(3):804-816. | ||||
REF 2 | Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface. Proteins. 2016 Sep;84(9):1246-56. | ||||
REF 3 | Structural Insights of Stereospecific Inhibition of Human Acetylcholinesterase by VX and Subsequent Reactivation by HI-6. Chem Res Toxicol. 2018 Dec 17;31(12):1405-1417. | ||||
REF 4 | Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents | ||||
REF 5 | Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents | ||||
REF 6 | Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents |
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