SMTL ID : 7z9g.1

E.coli gyrase holocomplex with 217 bp DNA and Albi-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain B: D.499, D.501 Chain E: T.14 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

1 x IM0: 4-[[3-(2-azanylethoxy)-2-oxidanyl-4-[[5-[[(2~{S})-2-[[4-[(6-oxidanylnaphthalen-2-yl)carbonylamino]phenyl]carbonylamino]-3-(1~{H}-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic acid(Non-covalent)

IM0.2: 35 residues within 4Å: Chain A: K.65, A.67, R.68, V.70, G.71, I.74, G.75, H.80, G.81, D.82, S.83, M.120 Chain B: K.448, G.449, D.499, K.741, G.742, L.743, G.744, E.745 Chain C: K.65, A.67, R.68, V.70, G.71, I.74, G.75, D.82, M.120, R.121, Y.122 Chain E: T.14 Chain G: C.4, A.5 Chain H: G.1 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:K.448, C:A.67 Hydrogen bonds: B:K.741, B:G.744, C:R.121, A:D.82

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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