SMTL ID : 6fqs.1

3.11A complex of S.Aureus gyrase with imidazopyrazinone T3 and DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 2 residues within 4Å: Chain A: D.100, D.102 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.100, A:D.102, H2O.1, H2O.1, H2O.1, H2O.1 MN.7: 2 residues within 4Å: Chain C: D.100, D.102 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.100, C:D.102, H2O.3, H2O.3, H2O.3, H2O.5

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

NA.2: 3 residues within 4Å: Chain B: Y.321, T.324, Q.327 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.324, B:Q.327, B:Q.327

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain B: F.96, S.111, M.112, G.114, Q.266 Chain E: A.4, G.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.112, B:G.114 GOL.4: 4 residues within 4Å: Chain B: R.136, D.137, N.139, K.140 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.137, B:N.139, B:N.139 GOL.5: 3 residues within 4Å: Chain B: E.250, G.254, Q.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.256 Water bridges: B:E.250, B:E.250 GOL.6: 3 residues within 4Å: Chain A: R.188 Chain B: R.237, I.335 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.237, A:R.188 GOL.9: 5 residues within 4Å: Chain D: P.43, R.46, R.47, E.155, P.156 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.46, D:R.47 GOL.10: 4 residues within 4Å: Chain D: E.250, G.254, R.255, Q.256 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.254, D:Q.256 GOL.11: 5 residues within 4Å: Chain D: R.251, R.255, T.289, R.308, K.309 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.251, D:R.255, D:K.309 GOL.12: 3 residues within 4Å: Chain E: G.3, A.4, G.5 No protein-ligand interaction detected (PLIP)

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

SO4.8: 3 residues within 4Å: Chain B: R.428 Chain D: R.428, R.431 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.428, D:R.431, B:R.428

2 x E3E: 5-cyclopropyl-8-fluoranyl-7-pyridin-4-yl-imidazo[1,2-a]quinoxalin-4-one(Non-covalent)

E3E.13: 8 residues within 4Å: Chain A: R.50 Chain B: S.83 Chain D: R.121, Y.122 Chain E: T.8, G.9 Chain F: C.12, A.13 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D pi-Cation interactions: A:R.50 Hydrogen bonds: B:S.83, D:R.121, D:R.121 E3E.14: 7 residues within 4Å: Chain C: R.50, G.51 Chain D: S.83 Chain E: C.12, A.13 Chain F: T.8, G.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.83

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
D

B
A

D
C

DNA gyrase subunit B,DNA gyrase subunit B

DNA gyrase subunit A

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