SMTL ID : 5cdn.1 (1 other biounit)

2.8A structure of etoposide with S.aureus DNA gyrase and DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-2-2-mer

Ligands

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

DG-DA-DG-DC-DG-DT-DA-DC.1: 30 residues within 4Å: Chain C: R.24, K.34, V.36, H.37, H.70, H.72, G.73, S.76, A.80, R.83, S.164, I.166, Q.258, R.263 Chain D: E.19, G.43, K.44, D.96, I.100 Chain F: G.5, T.6, A.7, C.8, G.9, C.10, T.11, C.12 Ligands: GOL.5, GOL.9, EVP.11 No protein-ligand interaction detected (PLIP) DG-DA-DG-DC-DG-DT-DA-DC.2: 29 residues within 4Å: Chain A: R.24, K.34, V.36, H.37, H.70, P.71, H.72, G.73, S.76, A.80, R.83, S.164, I.166, Q.258, R.263 Chain B: E.19, G.43, K.44, D.96, I.100 Chain E: G.5, T.6, A.7, C.8, G.9, C.10, T.11, C.12 Ligands: EVP.10 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.44, B:K.44, B:N.47, B:N.47, A:G.169, A:S.231, A:S.321 Water bridges: B:R.42, B:N.47, B:K.50, B:K.50, B:N.59, A:R.229 Salt bridges: B:K.50, B:K.50, B:R.55, B:R.55, B:H.99, B:R.179, A:R.229 Hydrophobic interactions: A:I.166

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

SO4.3: 6 residues within 4Å: Chain A: P.35, R.38, R.39, I.138, E.147, S.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.147 Water bridges: A:E.147 Salt bridges: A:R.38, A:R.39

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

MN.4: 3 residues within 4Å: Chain B: E.19, D.92, D.94 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.94, H2O.3, H2O.4, H2O.4, H2O.4 MN.8: 3 residues within 4Å: Chain D: E.19, D.92, D.94 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.94, H2O.7, H2O.8, H2O.8, H2O.8

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain C: M.104, G.106, V.259, N.260 Ligands: DG-DA-DG-DC-DG-DT-DA-DC.1, DG-DA-DG-DC-DG-DT-DA-DC.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.259, C:N.260 GOL.7: 3 residues within 4Å: Chain C: R.368, L.375, R.423 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.368 Water bridges: C:R.420 GOL.9: 6 residues within 4Å: Chain F: T.6, A.7 Ligands: DG-DA-DG-DC-DG-DT-DA-DC.1, DG-DA-DG-DC-DG-DT-DA-DC.1, DG-DA-DG-DC-DG-DT-DA-DC.1, DG-DA-DG-DC-DG-DT-DA-DC.1 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain C: Y.313, K.314, T.316, Q.319 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.314

2 x EVP: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside(Non-covalent)

EVP.10: 13 residues within 4Å: Chain A: S.75, E.79 Chain B: G.20, D.21, L.41, R.42, G.43 Chain C: Y.114 Chain E: C.4, G.5 Chain F: G.1, G.2 Ligands: DG-DA-DG-DC-DG-DT-DA-DC.2 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.42, A:E.79 Hydrogen bonds: B:D.21, B:R.42, B:G.43 Water bridges: B:S.22 EVP.11: 13 residues within 4Å: Chain A: Y.114 Chain C: S.75, E.79 Chain D: G.20, D.21, L.41, R.42, G.43 Chain E: G.1, G.2 Chain F: C.4, G.5 Ligands: DG-DA-DG-DC-DG-DT-DA-DC.1 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.21, D:D.21, D:G.43, C:S.75

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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