SMTL ID : 5zxm.1

Crystal Structure of GyraseB N-terminal at 1.93A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 23 residues within 4Å: Chain A: N.46, E.50, D.73, G.77, I.78, I.94, A.100, G.101, G.102, K.103, Y.109, G.114, L.115, H.116, G.117, V.118, G.119, V.120, S.121, T.165 Chain B: Y.5, I.10 Ligands: MG.5 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.46, A:D.73, A:G.102, A:K.103, A:Y.109, A:G.114, A:G.117, A:V.118, A:G.119, A:V.120, A:S.121, A:T.165, B:Y.5 Water bridges: A:A.47, A:D.73, A:A.100, A:G.101, A:H.116, A:H.116 Salt bridges: A:K.103 pi-Cation interactions: A:K.103 ADP.6: 21 residues within 4Å: Chain A: Y.5, I.10 Chain B: N.46, E.50, D.73, I.78, I.94, A.100, G.101, G.102, K.103, Y.109, G.114, L.115, H.116, G.117, V.118, G.119, V.120, S.121, T.165 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.46, B:D.73, B:G.102, B:K.103, B:Y.109, B:G.114, B:G.117, B:G.119, B:V.120, B:S.121, B:T.165, A:Y.5 Water bridges: B:E.42, B:N.46, B:N.46, B:A.47, B:D.73, B:G.77, B:A.100, B:G.101, B:K.103, B:V.118, B:V.118 Salt bridges: B:K.103 pi-Cation interactions: B:K.103

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: P.79, T.80, G.81, R.136 Chain B: D.6, S.7 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.80, A:T.80, A:G.81, B:S.7, B:S.7 Salt bridges: A:R.136 SO4.7: 7 residues within 4Å: Chain A: D.6, S.7 Chain B: P.79, T.80, G.81, R.136, D.137 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.80, B:T.80, B:G.81, A:S.7 Water bridges: B:T.80 Salt bridges: B:R.136

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: K.11, L.13, D.17, R.20, K.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.11, A:K.11 Water bridges: A:D.17, A:K.21 PEG.4: 3 residues within 4Å: Chain A: R.20, H.147, V.149 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.20, A:E.146 PEG.8: 4 residues within 4Å: Chain B: P.235, I.236, H.237, P.238 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: N.46, K.103 Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain B: L.13, D.17, R.20, K.21 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.20, B:K.21, B:K.21 GOL.10: 5 residues within 4Å: Chain B: T.290, T.311, G.312, D.313, R.316 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.311, B:G.312, B:D.313, B:D.313, B:R.316 Water bridges: B:R.286, B:R.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gupta, D. et al., Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain. Arch.Biochem.Biophys. (2021)

Release Date

2019-05-22

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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