SMTL ID : 6fqv.2 (1 other biounit)

2.60A BINARY COMPLEX OF S.AUREUS GYRASE with UNCLEAVED DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-2-2-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.31, P.43, R.46, R.47, E.155, P.156, S.157 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.46, A:E.155 Water bridges: A:L.41, A:R.46, A:E.155 GOL.2: 4 residues within 4Å: Chain A: D.95, M.112, P.218, R.484 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.484, A:R.484 GOL.3: 3 residues within 4Å: Chain A: N.53, E.54, N.139 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.53, A:N.53, A:E.54, A:N.139 GOL.5: 6 residues within 4Å: Chain C: P.43, R.46, R.47, E.155, P.156, S.157 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.46, C:P.156 Water bridges: C:V.30 GOL.6: 4 residues within 4Å: Chain C: R.245, E.262, R.483, R.484 No protein-ligand interaction detected (PLIP) GOL.9: 7 residues within 4Å: Chain C: D.23, S.27 Chain D: A.101, D.102, V.103, K.139, L.200 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.27, D:D.102, D:L.200 Water bridges: D:L.200 GOL.10: 5 residues within 4Å: Chain E: T.14, A.15 Chain F: G.5, T.6, A.7 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: Y.321, K.322, T.324, Q.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.321, A:T.324, A:Q.327 NA.8: 4 residues within 4Å: Chain C: Y.321, K.322, T.324, Q.327 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.321, C:T.324, C:Q.327

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain A: R.428 Chain C: R.428 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.428, C:R.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Germe, T. et al., A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance. Nucleic Acids Res. (2018)

Release Date

2018-04-04

Peptides

DNA gyrase subunit A: AC
DNA gyrase subunit B,DNA gyrase subunit B: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

C
T

B
S

D
U

DNA gyrase subunit A

DNA gyrase subunit B,DNA gyrase subunit B

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