SMTL ID : 4z3o.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.44 Å

Oligo State

homo-dimer

Ligands

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

DC-DA-DT-DG-DA-DA-DT.1: 27 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 C: A.5, T.6, T.7, C.8, A.9, T.10, G.11 Ligands: MG.5, MG.6, MFX.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.33, B:S.34, B:A.35, A:P.359 DC-DA-DT-DG-DA-DA-DT.2: 26 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, T.414, I.416, E.508 Chain C: A.1 Chain D: A.5, T.6, G.7, C.8, A.9, C.10, G.11 Ligands: MG.3, MFX.8 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.224 Hydrogen bonds: A:N.59, A:N.59, A:N.71, A:G.419, A:R.481, A:N.572 Salt bridges: A:K.62, A:K.62, A:H.111, A:R.227, A:R.228, A:K.479

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

MG.3: 3 residues within 4Å: Chain A: D.104, D.106 Ligands: DC-DG-DT-DG-DC-DA-DT.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.104, A:D.106 MG.4: 1 residues within 4Å: Ligands: MFX.8 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: MFX.8 MG.5: 3 residues within 4Å: Chain B: D.104, D.106 Ligands: DC-DA-DT-DG-DA-DA-DT.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.104, B:D.106 MG.6: 3 residues within 4Å: Chain B: S.325 Ligands: DC-DA-DT-DG-DA-DA-DT.1, MFX.7 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: MFX.7

2 x MFX: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

MFX.7: 10 residues within 4Å: Chain A: R.363 Chain B: R.54, G.55, E.73, S.325 Chain C: C.4, A.5 Chain D: G.1 Ligands: DC-DA-DT-DG-DA-DA-DT.1, MG.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.54 Hydrogen bonds: B:S.325 Salt bridges: A:R.363 MFX.8: 8 residues within 4Å: Chain A: R.54, E.73, S.325 Chain C: A.1 Chain D: T.4, A.5 Ligands: DC-DG-DT-DG-DC-DA-DT.2, MG.4 1 PLIP interactions: 1 interactions with chain B Salt bridges: B: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,ParE30-ParC55 fused topo IV from S. pneumoniae: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase 4 subunit B,ParE30-ParC55 fused topo IV from S. pneumoniae

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