SMTL ID : 5bti.1

Crystal structure of a topoisomerase II complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain B: E.37, D.110, D.112 Chain E: T.10 Chain G: T.10 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.110, B:D.112, H2O.4, H2O.5, H2O.5, H2O.12 MG.2: 4 residues within 4Å: Chain C: S.89 Chain F: T.10, A.11 Ligands: LFX.6 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 Ligand-Water interactions Metal complexes: LFX.6, H2O.7, H2O.11, H2O.11, H2O.11 MG.3: 5 residues within 4Å: Chain D: E.37, D.110, D.112 Chain F: T.10 Chain H: T.10 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.110, H2O.9, H2O.9, H2O.10, H2O.10 MG.5: 4 residues within 4Å: Chain A: S.89 Chain E: T.10 Chain G: T.10 Ligands: LFX.4 No protein-ligand interaction detected (PLIP)

2 x LFX: (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid(Non-covalent)

LFX.4: 16 residues within 4Å: Chain A: S.89, S.90 Chain B: R.60, G.61, T.78, E.79 Chain C: Y.128 Chain E: T.10, G.11 Chain F: C.14, A.15 Chain G: T.10, A.11 Chain H: T.14, A.15 Ligands: MG.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:E.79 Water bridges: A:S.89, A:S.89 LFX.6: 17 residues within 4Å: Chain A: R.127, Y.128 Chain C: S.89, S.90 Chain D: R.60, G.61, T.78, E.79 Chain E: T.14, A.15 Chain F: T.10, A.11 Chain G: C.14, A.15 Chain H: T.10, G.11 Ligands: MG.2 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.89 Water bridges: C:S.89, C:S.89, C:S.89 Salt bridges: D:E.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blower, T.R. et al., Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-02

Peptides

DNA gyrase subunit A: AC
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

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