SMTL ID : 4koe.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

hetero-oligomer

Ligands

1 x DC- DA- DT- DG- DA- DA- DT: E-site DNA1(Non-covalent)

DC-DA-DT-DG-DA-DA-DT.1: 27 residues within 4Å: Chain A: R.28, K.38, V.40, Q.41, H.74, H.76, G.77, S.80, A.84, R.87, K.93, T.168, I.170, E.262 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: TR6.9 25 PLIP interactions: 8 interactions with chain A, 8 interactions with chain D, 2 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: A:I.170, C:V.247, B:I.170 Hydrogen bonds: A:A.115, A:R.117, A:G.173, A:R.235, A:R.235, A:N.326, D:D.56, D:S.57, C:N.82, C:N.82, C:N.94, B:A.115, B:G.173, B:R.235, B:R.235, D:K.79, D:N.82, D:N.82, D:N.94, C:D.56, C:S.57 Salt bridges: A:K.233, C:K.85, C:K.85, C:H.134, C:R.250, C:R.251, B:K.233, B:K.233, D:K.85, D:K.85, D:H.134, D:R.250

1 x DC- DG- DT- DG- DC- DA- DT: E-site DNA3(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, E.262 Chain D: E.54, G.78, K.79, D.131 Chain F: A.5, T.6, G.7, C.8, A.9, C.10, G.11 Ligands: MG.6, TR6.10 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: 1 residues within 4Å: Ligands: TR6.9 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: 2 residues within 4Å: Ligands: DC-DG-DT-DG-DC-DA-DT.2, TR6.10 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: 2 residues within 4Å: Chain D: D.127, D.129 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.127, D:D.129

2 x TR6: Trovafloxacin(Non-covalent)

TR6.9: 11 residues within 4Å: Chain A: S.79 Chain B: R.117 Chain C: G.55, D.56, 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 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Salt bridges: B:R.117 Hydrogen bonds: A:S.79, C:R.77 Hydrophobic interactions: C:R.77 TR6.10: 12 residues within 4Å: Chain A: R.117 Chain B: S.79 Chain D: G.55, D.56, 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 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:R.77 Hydrogen bonds: D:R.77, B:S.79 Salt bridges: A:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laponogov, I. et al., Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions. To be Published

Release Date

2014-11-26

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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