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

2.95A structure of Moxifloxacin with S.aureus DNA gyrase and DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

hetero-oligomer

Ligands

7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: MFX.11 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.5, H2O.5, H2O.5, H2O.6, MFX.11 MG.2: 4 residues within 4Å: Chain A: Y.313, K.314, T.316, Q.319 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.313, A:T.316, A:Q.319 MG.5: 2 residues within 4Å: Chain B: D.95, D.97 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.95, B:D.97, H2O.2, H2O.3, H2O.3 MG.6: 3 residues within 4Å: Chain E: T.8, G.9 Ligands: MFX.12 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.5, H2O.6, H2O.6, H2O.6, MFX.12 MG.7: 4 residues within 4Å: Chain C: Y.313, K.314, T.316, Q.319 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:Y.313, C:T.316, C:Q.319 MG.10: 2 residues within 4Å: Chain D: D.95, D.97 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.95, D:D.97, H2O.5, H2O.5, H2O.5 MG.13: 2 residues within 4Å: Chain F: A.2 Ligands: MFX.14 3 PLIP interactions: 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.6, H2O.6, MFX.14

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.139, G.143, N.144, E.145, R.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.143 GOL.4: 5 residues within 4Å: Chain A: R.376, L.379, D.380, R.429, E.433 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.433, A:E.433, A:E.433 GOL.8: 5 residues within 4Å: Chain C: D.139, G.143, N.144, E.145, R.146 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.145 GOL.9: 4 residues within 4Å: Chain C: R.368, L.375, A.415, R.423 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.368, C:R.368, C:A.415, C:R.423

3 x MFX: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)(Non-functional Binders)

MFX.11: 11 residues within 4Å: Chain A: S.75 Chain B: R.45, G.46, E.64 Chain C: R.113, Y.114 Chain E: C.12, A.13 Chain F: T.8, G.9 Ligands: MG.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.75 Salt bridges: C:R.113 MFX.12: 12 residues within 4Å: Chain A: R.113, Y.114 Chain C: S.75 Chain D: D.24, R.45, G.46, E.64 Chain E: T.8, G.9 Chain F: C.12, A.13 Ligands: MG.6 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:S.75 Hydrophobic interactions: D:R.45 Salt bridges: A:R.113 MFX.14: 4 residues within 4Å: Chain E: T.19 Chain F: G.1, A.2 Ligands: MG.13 No protein-ligand interaction detected (PLIP)

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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