SMTL ID : 5btf.1

Crystal structure of a topoisomerase II complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-2-2-mer

Ligands

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

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.4, H2O.4, H2O.5 MG.2: 4 residues within 4Å: Chain C: S.89 Chain F: A.11 Chain H: G.11 Ligands: GFN.6 No protein-ligand interaction detected (PLIP) MG.3: 6 residues within 4Å: Chain D: E.37, D.110, D.112, D.114 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.6, H2O.6, H2O.7, H2O.7 MG.4: 6 residues within 4Å: Chain A: S.89 Chain E: T.10, G.11 Chain G: A.11 Chain H: A.15 Ligands: GFN.5 No protein-ligand interaction detected (PLIP)

2 x GFN: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

GFN.5: 17 residues within 4Å: Chain A: S.89 Chain B: D.39, R.60, G.61, T.78, E.79 Chain C: R.127, 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.4 7 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:E.79 Water bridges: B:T.78, A:S.89, A:S.89, A:S.89, A:S.89 Salt bridges: C:R.127 GFN.6: 18 residues within 4Å: Chain A: R.127, Y.128 Chain C: S.89, S.90 Chain D: D.39, 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 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:S.89 Salt bridges: A:R.127 Hydrophobic interactions: 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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