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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

hetero-1-2-1-mer

Ligands

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

MN.1: 2 residues within 4Å: Chain A: D.99, D.101 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.99, A:D.101, H2O.1, H2O.1, H2O.1, H2O.2 MN.2: 2 residues within 4Å: Chain C: D.100, D.102 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.100, C:D.102, H2O.1, H2O.1, H2O.1

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

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

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: 10 residues within 4Å: Chain B: R.121, Y.122 Chain C: R.50, G.51, E.69 Chain D: S.83 Chain E: T.8, G.9 Chain F: C.12, A.13 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:S.83, B:R.121, B:R.121, C:E.69, C:E.69 E32.6: 10 residues within 4Å: Chain A: R.49, G.50, E.68 Chain B: S.83 Chain D: R.121, Y.122 Chain E: C.12, A.13 Chain F: T.8, G.9 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:S.83, A:E.68, D:R.121, D:R.121 E32.7: 3 residues within 4Å: Chain E: T.19 Chain F: G.1, A.2 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain E: G.3, A.4, G.5, T.6 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: A
DNA gyrase subunit A: BD
DNA gyrase subunit B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

D
C

C
D

DNA gyrase subunit B

DNA gyrase subunit A

DNA gyrase subunit B

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