SMTL ID : 1kij.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x NOV: NOVOBIOCIN(Non-covalent)

NOV.1: 17 residues within 4Å: Chain A: N.43, D.46, E.47, D.70, R.73, G.74, I.75, P.76, D.78, I.91, K.100, F.101, K.107, V.115, R.133, T.164 Chain B: I.8 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.76, A:P.76, A:F.101, A:V.115, B:I.8, B:I.8 Hydrogen bonds: A:N.43, A:D.46, A:D.70, A:R.73, A:K.100, A:T.164 Water bridges: A:N.43, A:A.44, A:D.70, A:R.73, A:G.74, A:I.75, A:K.107, A:K.107 Salt bridges: A:R.73, A:K.107, A:R.133 pi-Cation interactions: A:R.73, A:R.73 NOV.3: 18 residues within 4Å: Chain A: I.8 Chain B: N.43, A.44, D.46, E.47, D.70, R.73, G.74, I.75, P.76, D.78, I.91, Y.92, F.101, V.115, A.117, R.133, T.164 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.76, B:P.76, B:I.91, B:F.101, B:F.101, B:V.115, A:I.8, A:I.8 Hydrogen bonds: B:N.43, B:D.70 Water bridges: B:D.46, B:E.47, B:E.47, B:D.70, B:R.73, B:R.133, B:R.133, B:T.164 Salt bridges: B:R.73, B:R.133 pi-Cation interactions: B:R.73, B:R.73

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 1 residues within 4Å: Chain A: S.288 No protein-ligand interaction detected (PLIP) FMT.4: 2 residues within 4Å: Chain B: S.288, N.292 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.292 Water bridges: B:S.288, B:S.288, B:S.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lamour, V. et al., An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. J.Biol.Chem. (2002)

Release Date

2002-06-03

Peptides

DNA GYRASE SUBUNIT B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA GYRASE SUBUNIT B