SMTL ID : 3raf.1

Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

hetero-oligomer

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: 26 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, 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: PDQ.7 22 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C, 7 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: A:I.170, B:I.170 Hydrogen bonds: A:G.173, A:N.326, A:N.326, C:K.79, C:N.82, C:N.82, C:N.94, D:D.56, D:S.57, C:D.56, C:S.57, C:R.77, C:R.77, B:R.117, B:G.173, D:N.82, D:N.82, D:N.94 Water bridges: A:Y.20 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: 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, 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, PDQ.8 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)

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: 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.5: 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.6: 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 PDQ: 3-AMINO-7-{(3R)-3-[(1S)-1-AMINOETHYL]PYRROLIDIN-1-YL}-1-CYCLOPROPYL-6-FLUORO-8-METHYLQUINAZOLINE-2,4(1H,3H)-DIONE(Non-covalent)

PDQ.7: 11 residues within 4Å: Chain A: S.79 Chain B: R.117, Y.118 Chain C: R.77, G.78, E.95, E.96 Chain E: C.4, A.5 Chain F: G.1 Ligands: DC-DA-DT-DG-DA-DA-DT.1 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.96, A:S.79 PDQ.8: 12 residues within 4Å: Chain A: R.117, Y.118 Chain B: S.79 Chain D: R.77, G.78, N.94, E.95, E.96 Chain E: A.1 Chain F: T.4, A.5 Ligands: DC-DG-DT-DG-DC-DA-DT.2 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:S.79, B:S.79, A:R.117, D:R.77

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

2012-03-28

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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