SMTL ID : 2xct.1 (1 other biounit)

THE TWINNED 3.35A STRUCTURE OF S. AUREUS GYRASE COMPLEX WITH CIPROFLOXACIN AND DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-dimer

Ligands

1 x DG- DT- DG- DC- DG- DG- DT: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'(Non-covalent)

DG-DT-DG-DC-DG-DG-DT.1: 26 residues within 4Å: Chain A: E.27, G.51, K.52, D.104, R.234, K.244, V.246, H.247, H.280, H.282, G.283, S.286, R.293, S.374, I.376, Q.468, R.473 Chain D: A.5, C.6, C.7, G.8, C.9, A.10, C.11, A.12 Ligands: CPF.6 25 PLIP interactions: 13 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:V.184, B:I.376, A:K.52, A:I.376 Hydrogen bonds: B:N.55, B:N.55, B:R.63, B:N.67, B:G.379, A:D.29, A:N.55, A:N.67, A:G.379, A:S.531 Salt bridges: B:K.58, B:K.58, B:R.63, B:H.107, B:R.187, B:R.439, A:K.58, A:K.58, A:R.63, A:H.107, A:R.187, A:R.439

1 x DG- DC- DC- DG- DT- DA- DG: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'(Non-covalent)

DG-DC-DC-DG-DT-DA-DG.2: 25 residues within 4Å: Chain B: E.27, G.51, K.52, D.104, I.108, R.234, K.244, V.246, H.247, H.280, H.282, G.283, S.286, R.293, S.374, I.376, Q.468 Chain C: C.5, C.6, A.7, C.8, G.9, G.10, C.11 Ligands: CPF.8 Protein-ligand interaction information (PLIP) not available

4 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3: 3 residues within 4Å: Chain A: E.27, D.100, D.102 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.102 MN.4: 2 residues within 4Å: Chain B: D.100, D.102 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.100, B:D.102 MN.5: 2 residues within 4Å: Chain D: G.1 Ligands: CPF.8 No protein-ligand interaction detected (PLIP) MN.7: 1 residues within 4Å: Ligands: CPF.6 No protein-ligand interaction detected (PLIP)

2 x CPF: 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID(Non-covalent)

CPF.6: 8 residues within 4Å: Chain A: R.50, G.51, S.285 Chain C: G.1 Chain D: C.4, A.5 Ligands: DG-DT-DG-DC-DG-DG-DT.1, MN.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.285 CPF.8: 8 residues within 4Å: Chain B: R.50, E.69, S.285 Chain C: C.4, C.5 Chain D: G.1 Ligands: DG-DC-DC-DG-DT-DA-DG.2, MN.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.50, B:S.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bax, B.D. et al., Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents. Nature (2010)

Release Date

2010-08-25

Peptides

DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A

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