SMTL ID : 7z9m.1

E.coli gyrase holocomplex with 217 bp DNA and Albi-1 (site AA)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

1 x IL1: 4-[[4-[[5-[[(2S)-2-[[5-[(4-cyanophenyl)carbonylamino]pyridin-2-yl]carbonylamino]-3-(1H-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]-2-oxidanyl-3-propan-2-yloxy-phenyl]carbonylamino]benzoic acid(Non-covalent)

IL1.1: 29 residues within 4Å: Chain A: K.65, A.67, R.68, G.71, I.74, G.75, M.120, R.121, Y.122 Chain C: K.65, A.67, R.68, V.70, G.71, I.74, H.80, G.81, D.82, M.120, R.121 Chain D: K.448, K.741, G.742, L.743, G.744, E.745 Chain F: A.14 Chain H: T.4, T.5 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:K.65, C:I.74 Salt bridges: C:K.65 Hydrogen bonds: D:G.744

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: D.499, D.501 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.501, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.3: 3 residues within 4Å: Chain D: D.499, D.501 Chain F: A.14 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.501, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michalczyk, E. et al., Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Nat Catal (2023)

Release Date

2023-02-15

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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