SMTL ID : 6j90.1

Crystal Structure of GyraseB N-Terminal Domain complex with ATP from Salmonella Typhi at 2.2A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 6 residues within 4Å: Chain A: D.6, S.7 Chain B: P.79, T.80, G.81, R.136 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: P.79, T.80, G.81, R.136 Chain B: D.6, S.7 Ligand excluded by PLIP

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 24 residues within 4Å: Chain A: E.42, 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, K.337 Chain B: Y.5, I.10 28 PLIP interactions: 27 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:L.115, A:H.116, A:H.116, A:G.117, A:V.118, A:G.119, A:V.120, A:S.121, A:T.165, B:Y.5 Water bridges: A:E.42, A:E.42, A:E.42, A:N.46, A:D.49, A:D.73, A:G.77, A:G.101, A:K.337, A:K.337 Salt bridges: A:K.103, A:K.337 pi-Cation interactions: A:K.103 ATP.9: 24 residues within 4Å: Chain A: Y.5, I.10 Chain B: E.42, 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, K.337 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.46, B:E.50, B:D.73, B:G.102, B:K.103, B:L.115, B:H.116, B:H.116, B:G.117, B:V.118, B:G.119, B:V.120, B:S.121, A:Y.5 Water bridges: B:E.42, B:E.42, B:N.46, B:D.49, B:D.73, B:D.73, B:D.73, B:G.77, B:T.165, B:K.337, B:K.337 Salt bridges: B:K.103, B:K.337 pi-Cation interactions: B:K.103

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.41, D.45, R.190, P.274, R.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.45, A:R.190, A:R.276, A:R.276 Water bridges: A:H.38, A:H.38 GOL.4: 9 residues within 4Å: Chain A: G.24, M.25, Y.26, G.28, H.38, Q.335, T.336 Chain B: S.333, S.334 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.24, A:Q.335, B:S.333 Water bridges: A:Y.26, A:H.38, A:E.42, A:E.42 GOL.10: 5 residues within 4Å: Chain B: F.41, D.45, R.190, P.274, R.276 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.45, B:R.190, B:R.276, B:R.276 GOL.11: 9 residues within 4Å: Chain A: S.333, S.334 Chain B: G.24, M.25, Y.26, G.28, H.38, Q.335, T.336 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.24, B:Q.335, A:S.333 Water bridges: B:Y.26, B:H.38, B:E.42, B:E.42

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

PEG.5: 3 residues within 4Å: Chain A: R.20, H.147, V.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.147 Water bridges: A:R.20, A:R.20, A:H.147 PEG.6: 4 residues within 4Å: Chain A: P.235, I.236, H.237, P.238 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.238, A:Q.257, A:S.366 PEG.7: 8 residues within 4Å: Chain A: T.72, D.73, V.133, Q.135, K.162, G.164, T.165, M.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.135 PEG.12: 3 residues within 4Å: Chain B: R.20, H.147, V.149 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.147 Water bridges: B:R.20, B:R.20, B:H.147 PEG.13: 4 residues within 4Å: Chain B: P.235, I.236, H.237, P.238 3 PLIP interactions: 3 interactions with chain B Water bridges: B:P.238, B:Q.257, B:S.366 PEG.14: 8 residues within 4Å: Chain B: T.72, D.73, V.133, Q.135, K.162, G.164, T.165, M.166 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaur, G. et al., Crystal Structure of GyraseB N-Terminal Domain complex with ATP from Salmonella Typhi at 2.2A Resolution. To Be Published

Release Date

2020-01-22

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA gyrase subunit B

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