SMTL ID : 6y8o.1

Mycobacterium smegmatis GyrB 22kDa ATPase sub-domain in complex with novobiocin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x NOV: NOVOBIOCIN(Non-covalent)

NOV.1: 14 residues within 4Å: Chain A: N.63, A.64, E.67, D.90, R.93, G.94, I.95, P.96, E.98, T.106, V.110, V.134, V.136, R.152 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.93, A:P.96, A:V.110, A:V.134 Hydrogen bonds: A:N.63, A:D.90 Water bridges: A:E.67, A:D.90, A:R.93, A:R.152, A:T.180 Salt bridges: A:R.93, A:R.152 pi-Cation interactions: A:R.93, A:R.93 NOV.11: 15 residues within 4Å: Chain B: N.63, A.64, D.66, E.67, D.90, R.93, G.94, I.95, P.96, E.98, T.106, V.110, V.136, R.152, T.180 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.96, B:V.110 Hydrogen bonds: B:N.63, B:D.90, B:T.106, B:T.180 Water bridges: B:D.66, B:D.90, B:R.93, B:R.93, B:R.93, B:R.93, B:R.93 Salt bridges: B:R.93, B:R.152 pi-Cation interactions: B:R.93, B:R.93

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: E.156, G.173, E.174, T.175 Chain B: D.83 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.173 EDO.3: 8 residues within 4Å: Chain A: F.158, Q.159, Y.160, K.168, K.170 Chain B: R.145, Y.160, D.162 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.159, A:Y.160, B:R.145, B:R.145 EDO.4: 1 residues within 4Å: Chain A: F.210 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: R.152, D.153, T.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.153, A:D.153, A:D.153 EDO.6: 4 residues within 4Å: Chain A: G.214, H.231, P.233, G.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.234 Water bridges: A:H.231 EDO.12: 5 residues within 4Å: Chain A: D.83 Chain B: E.156, G.173, E.174, T.175 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.175 Water bridges: B:G.173, B:E.174, B:E.174 EDO.13: 5 residues within 4Å: Chain B: Q.206, V.229, F.230, H.231, Y.232 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.229, B:H.231 EDO.14: 5 residues within 4Å: Chain B: Y.44, E.59, G.135, V.138 Ligands: NA.20 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.44, B:E.59 EDO.15: 5 residues within 4Å: Chain B: R.75, D.77, R.89, D.90, D.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.89 EDO.16: 4 residues within 4Å: Chain B: G.49, E.50, E.192 Ligands: ACT.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.50, B:E.50, B:E.192, B:E.192

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain A: T.175, K.176, E.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.175, A:K.176 ACT.8: 5 residues within 4Å: Chain A: S.47, G.49, E.50, R.51, G.52 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.47, A:S.47, A:G.49, A:E.50, A:R.51, A:G.52 Salt bridges: A:R.51 ACT.17: 7 residues within 4Å: Chain B: S.47, T.48, G.49, E.50, R.51, G.52 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.49, B:R.51, B:G.52 Water bridges: B:E.50

5 x NA: SODIUM ION(Non-functional Binders)

NA.9: 3 residues within 4Å: Chain A: D.91, G.92, T.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.92, A:T.178, A:T.178 NA.10: 2 residues within 4Å: Chain A: E.147 Chain B: E.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.147 NA.18: 3 residues within 4Å: Chain B: D.91, G.92, T.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.178, B:T.178 NA.19: 1 residues within 4Å: Chain B: E.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.59 NA.20: 2 residues within 4Å: Chain B: Y.44 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, S.R. et al., Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. J.Antimicrob.Chemother. (2020)

Release Date

2020-08-12

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B