SMTL ID : 4kpe.1

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.43 Å

Oligo State

hetero-2-2-mer

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 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.7, AF5.9 19 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A, 8 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: C:V.247, A:I.170 Hydrogen bonds: C:K.79, C:N.82, C:N.82, C:N.94, A:G.173, D:D.56, D:S.57, D:R.77, D:K.79, D:N.82, D:N.82, D:N.94, B:A.115, B:G.173, C:D.56, C:S.57, C:R.77 Salt bridges: C:K.85, C:K.85, C:H.134, C:R.250, C:R.251, A:K.233, A:K.233, D:K.85, D:K.85, D:H.134, D:R.250, B:K.233, B:K.233

1 x DC- DG- DT- DG- DC- DA- DT: E-site DNA3(Non-covalent)

DC-DG-DT-DG-DC-DA-DT.2: 28 residues within 4Å: Chain B: 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 Chain D: E.54, G.78, K.79, D.131, I.135 Chain F: A.5, T.6, G.7, C.8, A.9, C.10, G.11 Ligands: MG.6, MG.8, AF5.10 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: AF5.9 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: 3 residues within 4Å: Chain B: S.79 Ligands: DC-DG-DT-DG-DC-DA-DT.2, AF5.10 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: D.127, D.129 Ligands: DC-DA-DT-DG-DA-DA-DT.1 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 AF5: (7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid(Non-covalent)

AF5.9: 10 residues within 4Å: Chain A: S.79 Chain B: R.117 Chain C: R.77, G.78, E.96 Chain E: C.4, A.5 Chain F: G.1 Ligands: DC-DA-DT-DG-DA-DA-DT.1, MG.4 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:R.77, A:S.79, B:R.117 AF5.10: 10 residues within 4Å: Chain A: R.117 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 A, 1 interactions with chain B, 1 interactions with chain D Salt bridges: A:R.117 Hydrogen bonds: B:S.79, D:R.77

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

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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