Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T81503 | Target Info | |||
| Target Name | Bacterial DNA gyrase B (Bact gyrB) | ||||
| Synonyms | gyrB; DNA gyrase subunit B | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | Bact gyrB | ||||
| Biochemical Class | ATP-hydrolyzing DNA topoisomerase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | AMP-PNP | Ligand Info | |||
| Canonical SMILES | C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N | ||||
| InChI | 1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1 | ||||
| InChIKey | PVKSNHVPLWYQGJ-KQYNXXCUSA-N | ||||
| PubChem Compound ID | 33113 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 4WUB N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl condition | ||||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [1] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 SATGDDAREG 318 LIAVVSVKVP328 DPKFSSQTKD338 KLVSSEVKSA348 VEQQMNELLA358 EYLLENPTDA 368 KIVVGKIIDA378 ARAREAARRA388 REMT
|
|||||
|
|
GLU42
3.574
ASN46
2.881
ALA47
4.212
ASP49
4.755
GLU50
3.228
ASP73
2.799
GLY77
3.895
ILE78
3.403
PRO79
4.730
ILE94
3.251
ALA100
3.490
GLY101
3.672
GLY102
2.871
LYS103
2.838
|
|||||
| PDB ID: 4WUC N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 SATGDDAREG 318 LIAVVSVKVP328 DPKFSSQTKD338 KLVSSEVKSA348 VEQQMNELLA358 EYLLENPTDA 368 KIVVGKIIDA378 ARAREAARRA388 REMT
|
|||||
|
|
GLU42
3.592
ASN46
2.949
ALA47
4.202
ASP49
4.643
GLU50
3.283
ASP73
2.846
GLY77
3.887
ILE78
3.380
PRO79
4.729
ILE94
3.320
ALA100
3.609
GLY101
3.683
GLY102
2.895
LYS103
2.803
|
|||||
| PDB ID: 4WUD N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from no salt condition | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [1] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 SATGDDAREG 318 LIAVVSVKVP328 DPKFSSQTKD338 KLVSSEVKSA348 VEQQMNELLA358 EYLLENPTDA 368 KIVVGKIIDA378 ARAREAARRA388 REMT
|
|||||
|
|
GLU42
3.591
ASN46
2.971
ALA47
4.344
ASP49
4.666
GLU50
3.338
ASP73
2.835
GLY77
3.936
ILE78
3.465
PRO79
4.716
ILE94
3.374
ALA100
3.508
GLY101
3.686
GLY102
2.972
LYS103
2.854
|
|||||
| PDB ID: 4XTJ N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl plus 100 mM NaCl condition | ||||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [1] |
| PDB Sequence |
SYDSSSIKVL
13 KGLDAVRKRP23 GMYIGDTDDG33 TGLHHMVFEV43 VDNAIDEALA53 GHCKEIIVTI 63 HADNSVSVQD73 DGRGIPTGIH83 PEEGVSAAEV93 IMTVLHAGGK103 FDDNSYKVSG 113 GLHGVGVSVV123 NALSQKLELV133 IQREGKIHRQ143 IYEHGVPQAP153 LAVTGETEKT 163 GTMVRFWPSL173 ETFTNVTEFE183 YEILAKRLRE193 LSFLNSGVSI203 RLRDKRDGKE 213 DHFHYEGGIK223 AFVEYLNKNK233 TPIHPNIFYF243 STEKDGIGVE253 VALQWNDGFQ 263 ENIYCFTNNI273 PQRDGGTHLA283 GFRAAMTRTL293 NAYMDKEGYS303 SATGDDAREG 318 LIAVVSVKVP328 DPKFSSQTKD338 KLVSSEVKSA348 VEQQMNELLA358 EYLLENPTDA 368 KIVVGKIIDA378 ARAREAARRA388 REMT
|
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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 .ANP or .ANP2 or .ANP3 or :3ANP;style chemicals stick;color identity;select .A:42 or .A:46 or .A:47 or .A:49 or .A:50 or .A:73 or .A:77 or .A:78 or .A:79 or .A:94 or .A:100 or .A:101 or .A:102 or .A:103 or .A:109 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:120 or .A:121 or .A:165 or .A:335 or .A:337; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU42
3.523
ASN46
2.955
ALA47
4.261
ASP49
4.637
GLU50
3.266
ASP73
2.754
GLY77
3.929
ILE78
3.404
PRO79
4.719
ILE94
3.162
ALA100
3.496
GLY101
3.669
GLY102
2.963
LYS103
2.801
|
|||||
| PDB ID: 1EI1 DIMERIZATION OF E. COLI DNA GYRASE B PROVIDES A STRUCTURAL MECHANISM FOR ACTIVATING THE ATPASE CATALYTIC CENTER | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [2] |
| PDB Sequence |
SNSSDSSSIK
11 VLKGLDAVRK21 RPGMYIGDTD31 DGTGLHHMVF41 EVVDNAIDEA51 LAGHCKEIIV 61 TIHADNSVSV71 QDDGRGIPTG81 IHPEEGVSAA91 EVIMTVLHAG101 GKFDDNSYKV 111 SGGLHGVGVS121 VVNALSQKLE131 LVIQREGKIH141 RQIYEHGVPQ151 APLAVTGETE 161 KTGTMVRFWP171 SLETFTNVTE181 FEYEILAKRL191 RELSFLDSGV201 SIRLRDKRDG 211 KEDHFHYEGG221 IKAFVEYLNK231 NKTPIHPNIF241 YFSTEKDGIG251 VEVALQWNDG 261 FQENIYCFTN271 NIPQRDGGTH281 LAGFRAAMTR291 TLNAYMDKEG301 YSKKAKVSAT 311 GDDAREGLIA321 VVSVKVPDPK331 FSSQTKDKLV341 SSEVKSAVEQ351 QMNELLAEYL 361 LENPTDAKIV371 VGKIIDAARA381 REAARRAREM391 T
|
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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 .ANP or .ANP2 or .ANP3 or :3ANP;style chemicals stick;color identity;select .A:42 or .A:46 or .A:47 or .A:49 or .A:50 or .A:73 or .A:77 or .A:78 or .A:79 or .A:94 or .A:100 or .A:101 or .A:102 or .A:103 or .A:109 or .A:113 or .A:114 or .A:115 or .A:116 or .A:117 or .A:118 or .A:119 or .A:120 or .A:121 or .A:165 or .A:335 or .A:337; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU42
3.420
ASN46
2.992
ALA47
4.218
ASP49
4.857
GLU50
3.200
ASP73
2.587
GLY77
3.835
ILE78
3.392
PRO79
4.715
ILE94
3.711
ALA100
3.561
GLY101
3.142
GLY102
2.500
LYS103
2.770
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The role of monovalent cations in the ATPase reaction of DNA gyrase. Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):996-1005. | ||||
| REF 2 | Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. J Biol Chem. 2000 Mar 31;275(13):9468-75. | ||||
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