SMTL ID : 9ggq.1

E.coli gyrase holocomplex with cleaved chirally wrapped 217 bp DNA fragment and moxifloxacin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

4 x MG: MAGNESIUM ION

MG.1: 1 residues within 4Å: Ligands: MFX.6 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain B: D.499, D.501 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.501 MG.3: 1 residues within 4Å: Ligands: MFX.5 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain D: D.499, D.501 No protein-ligand interaction detected (PLIP)

2 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

MFX.5: 8 residues within 4Å: Chain A: R.121, Y.122 Chain D: G.449 Chain E: A.111 Chain F: T.103, T.104 Chain H: A.112 Ligands: MG.3 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:S.83, C:S.83, C:S.83 Salt bridges: A:R.121 MFX.6: 10 residues within 4Å: Chain B: K.448, G.449, E.467 Chain C: R.121, Y.122 Chain F: G.100 Chain G: T.99 Chain H: C.115, A.116 Ligands: MG.1 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Salt bridges: C:R.121 Water bridges: A:S.83, A:S.83, A:S.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalczyk, E. et al., Structural basis of chiral wrap and T-segment capture by Escherichia coli DNA gyrase. Proceedings of the National Academy of Sciences USA (2024)

Release Date

2024-09-11

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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