SMTL ID : 4z4q.1

Quinazolinedione(PD 0305970)-DNA cleavage complex of topoisomerase IV from S. pneumoniae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

homo-dimer

Ligands

2 x DG- DT- DA- DA- DT- DA- DC: V-site DNA(Non-covalent)

DG-DT-DA-DA-DT-DA-DC.1: 25 residues within 4Å: Chain A: E.31, G.55, K.56, D.108, R.274, K.284, V.286, H.320, H.322, G.323, S.326, A.330, R.333, K.339, T.414, I.416, E.508 Chain C: G.5, T.6, A.7, T.8, T.9, A.10, C.11 Ligands: PDQ.7 15 PLIP interactions: 2 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:I.416 Hydrogen bonds: A:K.56, A:N.59, A:N.59, A:N.71, A:R.363, A:G.419, A:R.481, B:S.34, B:N.59, B:N.59, B:N.71, B:G.419, B:R.481, B:R.481, A:S.34, A:R.54 Salt bridges: A:K.62, A:K.62, A:H.111, A:R.227, A:R.228, A:R.363, A:K.479, A:K.479, B:K.62, B:K.62, B:H.111, B:R.227, B:R.363, B:K.479, B:K.479 DG-DT-DA-DA-DT-DA-DC.2: 25 residues within 4Å: Chain B: E.31, G.55, K.56, D.108, R.274, K.284, V.286, H.320, H.322, G.323, S.326, A.330, R.333, K.339, T.414, I.416, E.508 Chain D: A.5, T.6, C.7, C.8, A.9, C.10, A.11 Ligands: 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.562, K.563, T.565, Q.568 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.562, A:T.565, A:Q.568 MG.4: 3 residues within 4Å: Chain A: E.31, D.104, D.106 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.104, A:D.106 MG.5: 4 residues within 4Å: Chain B: F.562, K.563, T.565, Q.568 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.565, B:Q.568 MG.6: 3 residues within 4Å: Chain B: E.31, D.104, D.106 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.104, B:D.106

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: R.54, G.55, E.72, E.73, S.325 Chain B: R.363, Y.364 Chain C: C.4, G.5 Chain D: G.1 Ligands: DG-DT-DA-DA-DT-DA-DC.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.73, A:S.325, B:R.363 PDQ.8: 11 residues within 4Å: Chain A: R.363, Y.364 Chain B: R.54, G.55, E.72, E.73, S.325 Chain C: A.1 Chain D: T.4, A.5 Ligands: DT-DG-DT-DG-DG-DA-DT.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.54, B:S.325, A:R.363, A:R.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laponogov, I. et al., Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae. To Be Published

Release Date

2016-09-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

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