SMTL ID : 4kpf.1

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

hetero-2-2-mer

Ligands

1 x DC- DA- DT- DG- DA- DA- DT: E-site1(Non-covalent)

DC-DA-DT-DG-DA-DA-DT.1: 27 residues within 4Å: Chain A: R.28, K.38, V.40, H.74, H.76, G.77, S.80, A.84, R.87, K.93, T.168, I.170 Chain C: E.54, G.78, K.79, D.131, I.135 Chain E: A.5, T.6, T.7, C.8, A.9, T.10, G.11 Chain F: G.1 Ligands: MG.6, 1UV.10 20 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A, 8 interactions with chain D, 3 interactions with chain B Hydrogen bonds: C:K.79, C:N.82, C:N.82, C:N.94, A:A.115, A:R.117, A:G.173, D:S.57, D:K.79, D:N.82, D:N.82, D:N.94, C:D.56, C:S.57, C:S.57, B:G.173 Salt bridges: C:K.85, C:K.85, C:H.134, C:R.250, C:R.251, A:K.233, A:K.233, D:K.85, D:K.85, D:H.134, D:R.250, B:K.233, B:K.233 Hydrophobic interactions: A:I.170

1 x DC- DG- DT- DG- DC- DA- DT: E-site3(Non-covalent)

DC-DG-DT-DG-DC-DA-DT.2: 27 residues within 4Å: Chain B: R.28, K.38, V.40, H.74, H.76, G.77, S.80, A.84, R.87, K.93, T.168, I.170 Chain D: E.54, G.78, K.79, D.131, I.135 Chain F: A.5, T.6, G.7, C.8, A.9, C.10, G.11 Ligands: MG.7, MG.8, 1UV.9 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: F.316, K.317, T.319, Q.322 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.316, A:K.317, A:T.319, A:Q.322 MG.4: 1 residues within 4Å: Ligands: 1UV.10 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: F.316, K.317, T.319, Q.322 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:F.316, B:K.317, B:T.319, B:Q.322 MG.6: 3 residues within 4Å: Chain C: D.127, D.129 Ligands: DC-DA-DT-DG-DA-DA-DT.1 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.127, C:D.129 MG.7: 4 residues within 4Å: Chain D: E.54, D.127, D.129 Ligands: DC-DG-DT-DG-DC-DA-DT.2 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.127, D:D.129 MG.8: 2 residues within 4Å: Ligands: DC-DG-DT-DG-DC-DA-DT.2, 1UV.9 No protein-ligand interaction detected (PLIP)

2 x 1UV: (3aS,4R)-4-amino-13-cyclopropyl-8-fluoro-10-oxo-3a,4,5,6,10,13-hexahydro-1H,3H-pyrrolo[2',1':3,4][1,4]oxazepino[5,6-h]quinoline-11-carboxylic acid(Non-covalent)

1UV.9: 10 residues within 4Å: Chain A: R.117 Chain B: S.79 Chain D: R.77, G.78, E.96 Chain E: A.1 Chain F: T.4, A.5 Ligands: DC-DG-DT-DG-DC-DA-DT.2, MG.8 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:S.79, D:R.77 Salt bridges: A:R.117 1UV.10: 11 residues within 4Å: Chain A: S.79 Chain B: R.117, Y.118 Chain C: R.77, G.78, E.96 Chain E: C.4, A.5 Chain F: G.1 Ligands: DC-DA-DT-DG-DA-DA-DT.1, MG.4 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:R.77, A:S.79 Salt bridges: B:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laponogov, I. et al., Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones. Open Biol (2016)

Release Date

2014-11-26

Peptides

ParC55: AB
ParE30: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ParC55

ParE30

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