SMTL ID : 5cdr.1

2.65 structure of S.aureus DNA gyrase and artificially nicked DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-2-2-mer

Ligands

1 x DA- DG- DC- DC- DG- DT- DA- DG: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3')(Non-covalent)

DA-DG-DC-DC-DG-DT-DA-DG.1: 29 residues within 4Å: Chain A: R.25, K.35, V.37, H.38, H.71, H.73, G.74, S.77, A.81, R.84, S.165, I.167, Q.259, R.264 Chain B: E.19, G.43, K.44, D.96, I.100 Chain E: G.2 Chain F: C.13, T.14, A.15, C.16, G.17, G.18, C.19 Ligands: GOL.9, GOL.10 Protein-ligand interaction information (PLIP) not available

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: Y.314, K.315, T.317, Q.320 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.314, A:T.317, A:Q.320, H2O.5, H2O.9 MN.5: 3 residues within 4Å: Chain B: E.19, D.92, D.94 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.92, B:D.94, H2O.10, H2O.11, H2O.12, H2O.23 MN.8: 3 residues within 4Å: Chain D: E.19, D.92, D.94 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.92, D:D.94, H2O.22, H2O.22, H2O.22

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: P.52, D.53, S.55, R.119 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.52, A:R.119, A:R.119 Water bridges: A:S.55, A:Y.56 GOL.4: 6 residues within 4Å: Chain A: D.88, F.89, M.105, P.211, T.212, R.477 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.88 GOL.6: 6 residues within 4Å: Chain C: A.24, P.36, R.39, R.40, E.148, P.149 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.39, C:E.148 Water bridges: C:E.148, C:S.150, C:S.150 GOL.7: 4 residues within 4Å: Chain C: E.243, G.247, R.248, Q.249 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.243, C:G.247 Water bridges: C:G.245, C:G.247, C:Q.249 GOL.9: 7 residues within 4Å: Chain A: F.89, S.104, M.105, G.107, Q.259, V.260 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.107, A:V.260 GOL.10: 6 residues within 4Å: Chain A: S.76 Chain E: G.2, T.3 Chain F: C.13 Ligands: DA-DG-DC-DC-DG-DT-DA-DG.1, DA-DG-DC-DC-DG-DT-DA-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, P.F. et al., Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin. Nat Commun (2015)

Release Date

2015-12-16

Peptides

DNA gyrase subunit A: AC
DNA gyrase subunit B,DNA gyrase subunit B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

DNA gyrase subunit A

DNA gyrase subunit B,DNA gyrase subunit B

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