- 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)
- 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)
- 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
AB
B
- 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)
- 1 x DC- DG- DT- DG- DC- DA- DT: DNA (5'-D(*CP*GP*TP*GP*CP*AP*T)-3')(Non-covalent)
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x TE9: delafloxacin
- 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
AB
B