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

3.06A COMPLEX OF S.AUREUS GYRASE with imidazopyrazinone T1 AND DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

hetero-2-2-mer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: E.26, D.99, D.101 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.1, H2O.1, H2O.1 MN.2: 3 residues within 4Å: Chain C: E.26, D.99, D.101 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.99, C:D.101, H2O.1, H2O.1, H2O.1

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

SO4.3: 5 residues within 4Å: Chain D: A.31, R.47, H.78, P.79, H.80 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.47, D:H.78, D:H.80

3 x E32: 7-[(3~{S})-3-azanylpyrrolidin-1-yl]-5-cyclopropyl-8-fluoranyl-imidazo[1,2-a]quinoxalin-4-one(Non-covalent)(Non-functional Binders)

E32.4: 8 residues within 4Å: Chain C: R.49, G.50, E.68 Chain D: S.83 Chain E: T.8, G.9 Chain F: C.12, A.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.68, D:S.83 E32.5: 8 residues within 4Å: Chain A: R.49 Chain B: S.83 Chain D: R.121, Y.122 Chain E: C.12, A.13 Chain F: T.8, G.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.83, D:R.121 E32.6: 3 residues within 4Å: Chain E: T.19 Chain F: G.1, A.2 No protein-ligand interaction detected (PLIP)

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: 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 A

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