SMTL ID : 6enh.1

Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with an aminocoumarin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x BHW: Coumermycin A1(Non-covalent)

BHW.1: 32 residues within 4Å: Chain A: I.43, N.46, A.47, D.49, E.50, V.71, E.72, D.73, R.76, G.77, I.78, P.79, I.94, R.136, T.167, V.169 Chain B: N.46, A.47, D.49, E.50, V.71, E.72, D.73, R.76, G.77, I.78, P.79, I.94, R.136, T.167, V.169 Ligands: BHW.4 31 PLIP interactions: 14 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:I.43, A:N.46, A:A.47, A:V.71, A:R.76, A:V.169, B:N.46, B:A.47, B:V.71, B:I.78, B:I.94, B:T.167, B:V.169 Hydrogen bonds: A:D.73, A:R.76, B:N.46, B:D.73, B:R.76, B:R.136, B:T.167 Water bridges: A:E.50, A:T.167, B:R.76 Salt bridges: A:R.76, A:R.136, B:R.76, B:R.136 pi-Cation interactions: A:R.76, A:R.76, B:R.76, B:R.76 BHW.4: 32 residues within 4Å: Chain A: N.46, A.47, D.49, E.50, V.71, E.72, D.73, R.76, G.77, I.78, P.79, I.94, R.136, T.167, V.169 Chain B: I.43, N.46, A.47, D.49, E.50, V.71, E.72, D.73, R.76, G.77, I.78, P.79, I.94, R.136, T.167, V.169 Ligands: BHW.1 31 PLIP interactions: 17 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:N.46, A:A.47, A:V.71, A:I.78, A:I.94, A:T.167, A:V.169, B:I.43, B:N.46, B:A.47, B:V.71, B:R.76, B:V.169 Hydrogen bonds: A:N.46, A:D.73, A:R.76, A:R.136, B:D.73, B:R.76, B:T.167 Water bridges: A:E.50, A:T.167, B:R.76 Salt bridges: A:R.76, A:R.136, B:R.76, B:R.136 pi-Cation interactions: A:R.76, A:R.76, B:R.76, B:R.76

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 3 residues within 4Å: Chain A: A.51, G.54, A.200 No protein-ligand interaction detected (PLIP) IMD.3: 4 residues within 4Å: Chain A: E.58, E.72, D.73, N.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.58 IMD.5: 3 residues within 4Å: Chain B: A.51, G.54, A.200 No protein-ligand interaction detected (PLIP) IMD.6: 4 residues within 4Å: Chain B: E.58, E.72, D.73, N.74 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanden Broeck, A. et al., Structural Basis for DNA Gyrase Interaction with Coumermycin A1. J.Med.Chem. (2019)

Release Date

2019-04-10

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA gyrase subunit B