SMTL ID : 3rad.1

Quinolone(Clinafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-2-2-mer

Ligands

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

DC-DA-DT-DG-DA-DA-DT.1: 28 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, N.267 Chain B: R.117 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 Ligands: MG.4, NFX.9 17 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C, 8 interactions with chain D, 4 interactions with chain B Hydrogen bonds: A:G.173, A:N.326, C:K.79, C:N.82, C:N.82, C:N.94, D:S.57, C:D.56, C:S.57, D:K.79, D:N.82, D:N.82, D:N.94, B:G.173 Salt bridges: A:K.233, C:K.85, C:K.85, C:H.134, C:R.250, C:R.251, D:K.85, D:K.85, D:H.134, D:R.250, B:R.117, B:K.233, B:K.233 Hydrophobic interactions: C:V.247

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

DC-DG-DT-DG-DC-DA-DT.2: 26 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 Chain E: A.1 Chain F: A.5, T.6, G.7, C.8, A.9, C.10, G.11 Ligands: MG.8, NFX.10 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.316, A:T.319, A:Q.322 MG.4: 2 residues within 4Å: Ligands: DC-DA-DT-DG-DA-DA-DT.1, NFX.9 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: F.316, K.317, T.319, Q.322 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:F.316, B:T.319, B:Q.322 MG.6: 1 residues within 4Å: Ligands: NFX.10 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain C: D.127, D.129 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.127, C:D.129 MG.8: 3 residues within 4Å: Chain D: 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

2 x NFX: 7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

NFX.9: 10 residues within 4Å: Chain A: S.79 Chain B: R.117, Y.118 Chain C: R.77, G.78 Chain E: C.4, A.5 Chain F: G.1 Ligands: DC-DA-DT-DG-DA-DA-DT.1, MG.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.79, B:R.117 NFX.10: 11 residues within 4Å: Chain A: R.117, Y.118 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.6 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:S.79, D:E.96 Salt bridges: A: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

2012-04-25

Peptides

DNA topoisomerase 4 subunit A: AB
DNA topoisomerase 4 subunit B: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DNA topoisomerase 4 subunit A

DNA topoisomerase 4 subunit B

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