SMTL ID : 7dqh.1

E. coli GyrB ATPase domain in complex with 2-hydroxybenzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

1 x AX7: 1H-benzimidazol-2-amine(Non-covalent)

AX7.1: 6 residues within 4Å: Chain A: R.5, H.132, E.159 Chain B: R.5, H.132, E.159 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Salt bridges: B:E.159, A:E.159 pi-Stacking: B:H.132, A:H.132 pi-Cation interactions: B:H.132, A:H.132 Hydrophobic interactions: A:H.132

2 x OHB: salicylamide(Non-covalent)

OHB.2: 10 residues within 4Å: Chain A: V.28, N.31, A.32, E.35, V.56, D.58, I.63, V.105, T.150, V.152 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.31, A:E.35, A:I.63, A:T.150 Hydrogen bonds: A:V.56, A:D.58, A:V.152 OHB.5: 10 residues within 4Å: Chain B: V.28, N.31, A.32, E.35, V.56, D.58, I.63, V.105, T.150, V.152 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.31, B:E.35, B:I.63, B:I.63, B:T.150 Hydrogen bonds: B:V.56, B:D.58, B:V.152

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: R.5, K.6, P.8 Chain B: P.135, Q.136 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Q.136 Hydrogen bonds: A:K.6 PO4.4: 3 residues within 4Å: Chain A: H.49, R.153, K.193 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.49, A:K.193 Salt bridges: A:H.49, A:R.153, A:K.193 PO4.6: 3 residues within 4Å: Chain B: H.49, R.153, K.193 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.49, B:R.153, B:K.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Y. et al., Identification of new building blocks by fragment screening for discovering GyrB inhibitors. Bioorg.Chem. (2021)

Release Date

2021-10-27

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA gyrase subunit B

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