SMTL ID : 8c41.1

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

1 x DC- DA- DT- DG- DA- DA- DT: DNA (5'-D(*CP*AP*TP*GP*AP*AP*T)-3')(Non-covalent)

DC-DA-DT-DG-DA-DA-DT.1: 32 residues within 4Å: Chain A: E.31, G.55, K.56, D.108, I.112, R.274, K.284, V.286, H.320, H.322, G.323, S.325, S.326, A.330, R.333, K.339, T.414, I.416, E.508, N.510 Chain B: R.363, Y.364 Chain C: A.5, T.6, T.7, C.8, A.9, T.10, G.11 Chain D: G.1 Ligands: MG.7, TE9.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.416 Hydrogen bonds: A:R.54, A:N.59, A:N.59, A:E.225, A:E.225, A:G.419, A:R.481, A:N.574, A:D.33, A:S.34, A:S.34, A:R.54 Water bridges: A:R.228, A:A.421, A:K.479, A:K.479 Salt bridges: A:K.62, A:K.62, A:K.70, A:H.111, A:R.227, A:R.228, A:K.479

1 x DC- DG- DT- DG- DC- DA- DT: DNA (5'-D(*CP*GP*TP*GP*CP*AP*T)-3')(Non-covalent)

DC-DG-DT-DG-DC-DA-DT.2: 34 residues within 4Å: Chain A: R.363, Y.364 Chain B: E.31, G.55, K.56, D.108, I.112, R.274, K.284, V.286, H.320, H.322, G.323, S.325, S.326, A.330, R.333, K.339, T.414, G.415, I.416, E.508, N.510, N.513 Chain C: A.1 Chain D: A.5, T.6, G.7, C.8, A.9, C.10, G.11 Ligands: MG.12, TE9.15 Protein-ligand interaction information (PLIP) not available

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: L.624, V.627, I.628, L.631, L.668, R.672, L.673, N.675, L.681 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.624, A:V.627, A:L.668, A:R.672, A:N.675 Hydrogen bonds: A:R.672, A:N.675 MPD.4: 9 residues within 4Å: Chain A: W.338, M.354, P.460, T.461, G.462, T.503, E.504, L.542, L.725 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.460, A:E.504 MPD.9: 11 residues within 4Å: Chain B: L.624, V.627, I.628, L.631, L.668, R.672, L.673, N.675, T.676, L.681 Ligands: CL.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.624, B:L.624, B:V.627, B:I.628, B:R.672, B:L.673 Hydrogen bonds: B:N.675

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

MG.5: 2 residues within 4Å: Chain A: S.325 Ligands: TE9.14 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain A: F.562, K.563, T.565, D.566, Q.568, I.569 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.563, A:T.565, A:Q.568, H2O.4, H2O.7 MG.7: 3 residues within 4Å: Chain A: D.104, D.106 Ligands: DC-DA-DT-DG-DA-DA-DT.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.104, A:D.106, H2O.1, H2O.1, H2O.2 MG.10: 3 residues within 4Å: Chain B: S.325, D.329 Ligands: TE9.15 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: F.562, K.563, T.565, D.566, Q.568 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:F.562, B:K.563, B:Q.568, H2O.14, H2O.15 MG.12: 3 residues within 4Å: Chain B: D.104, D.106 Ligands: DC-DG-DT-DG-DC-DA-DT.2 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.104, B:D.106, H2O.8, H2O.8, H2O.9

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: R.617, L.624, R.672 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: R.617, L.624, L.668, R.672 Ligands: MPD.9 Ligand excluded by PLIP

2 x TE9: delafloxacin

TE9.14: 13 residues within 4Å: Chain A: G.32, D.33, L.53, R.54, G.55, S.325 Chain B: R.363 Chain C: C.4, A.5 Chain D: G.1, A.2 Ligands: DC-DA-DT-DG-DA-DA-DT.1, MG.5 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.363 Hydrogen bonds: A:D.33, A:R.54, A:S.325 Halogen bonds: A:R.54 TE9.15: 13 residues within 4Å: Chain A: R.363 Chain B: G.32, D.33, L.53, R.54, G.55, S.325 Chain C: A.1, G.2 Chain D: T.4, A.5 Ligands: DC-DG-DT-DG-DC-DA-DT.2, MG.10 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Water bridges: A:R.363, B:S.325 Salt bridges: A:R.363 Hydrogen bonds: B:D.33, B:D.33, B:R.54, B:S.325 Halogen bonds: B:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Najmudin, S. et al., The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin. To Be Published

Release Date

2024-01-10

Peptides

Fused ParE30ParC55 CLEAVAGE COMPLEX of the TOPOISOMERASE IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fused ParE30ParC55 CLEAVAGE COMPLEX of the TOPOISOMERASE IV

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