- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x DT- DG- DT- DG- DG- DA- DT: DNA (5'-D(TP*GP*TP*GP*GP*AP*T)-3')(Non-covalent)
- 1 x DG- DT- DA- DA- DT- DA- DC: DNA (5'-D(GP*TP*AP*AP*TP*AP*C)-3')(Non-covalent)
DG-DT-DA-DA-DT-DA-DC.2: 31 residues within 4Å:- Chain B: E.31, G.55, K.56, D.108, I.112, R.274, K.284, V.286, Q.287, H.320, H.322, G.323, S.326, A.330, R.333, K.339, T.414, I.416, E.508, N.513
- Chain C: G.1
- Chain D: G.5, T.6, A.7, T.8, T.9, A.10, C.11
- Ligands: MG.15, MG.17, TE9.25
Protein-ligand interaction information (PLIP) not available- 6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.3: 2 residues within 4Å:- Chain A: S.325
- Ligands: TE9.24
No protein-ligand interaction detected (PLIP)MG.4: 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.7, H2O.13
MG.5: 3 residues within 4Å:- Chain A: D.104, D.106
- Ligands: DT-DG-DT-DG-DG-DA-DT.1
6 PLIP interactions:2 interactions with chain A, 4 Ligand-Water interactions- Metal complexes: A:D.104, A:D.106, H2O.1, H2O.4, H2O.7, H2O.39
MG.15: 3 residues within 4Å:- Chain B: S.325
- Ligands: DG-DT-DA-DA-DT-DA-DC.2, TE9.25
No protein-ligand interaction detected (PLIP)MG.16: 5 residues within 4Å:- Chain B: F.562, K.563, T.565, D.566, Q.568
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:F.562, B:T.565, B:Q.568, H2O.25
MG.17: 3 residues within 4Å:- Chain B: D.104, D.106
- Ligands: DG-DT-DA-DA-DT-DA-DC.2
6 PLIP interactions:2 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:D.104, B:D.106, H2O.21, H2O.23, H2O.27, H2O.27
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.7: 10 residues within 4Å:- Chain A: L.624, V.627, I.628, L.631, L.668, R.672, L.673, N.675, T.676, L.681
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:L.624, A:V.627, A:I.628, A:L.668
- Hydrogen bonds: A:R.672
MPD.8: 9 residues within 4Å:- Chain A: N.337, M.354, P.460, T.461, G.462, T.503, E.504, L.542, L.725
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:P.460
MPD.22: 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.18
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:L.624, B:V.627, B:I.628, B:L.668, B:T.676
- Hydrogen bonds: B:R.672
- 2 x MLA: MALONIC ACID(Non-covalent)
MLA.9: 4 residues within 4Å:- Chain A: L.618, H.619, E.622, R.689
6 PLIP interactions:6 interactions with chain A- Water bridges: A:H.619, A:H.619, A:R.689, A:R.689
- Salt bridges: A:H.619, A:R.689
MLA.11: 2 residues within 4Å:- Chain A: R.703, N.707
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.707
- Salt bridges: A:R.703
- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.10: 2 residues within 4Å:- Chain A: Y.375, Q.378
No protein-ligand interaction detected (PLIP)ACT.13: 2 residues within 4Å:- Chain A: P.443, Y.706
No protein-ligand interaction detected (PLIP)ACT.19: 2 residues within 4Å:- Chain B: P.443, Y.706
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.706
ACT.20: 9 residues within 4Å:- Chain B: T.205, I.206, E.207, D.208, R.211, A.212, S.254, L.255, E.256
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:I.206, B:A.212, B:L.255
- Hydrogen bonds: B:E.207, B:D.208, B:L.255, B:E.256
- Water bridges: B:S.254, B:S.254
- 4 x FMT: FORMIC ACID(Non-functional Binders)
FMT.12: 6 residues within 4Å:- Chain A: M.347, H.348, G.349, N.351
- Chain B: N.185, A.186
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:N.185, A:N.351
FMT.14: 5 residues within 4Å:- Chain A: T.667, L.668, Q.669, Y.671, R.672
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Q.669, A:Q.669, A:Y.671, A:R.672
FMT.21: 6 residues within 4Å:- Chain A: K.142, K.145, Q.188
- Chain B: Y.305, H.348, R.368
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:Y.305, B:H.348, B:R.368, A:K.142, A:K.145, A:Q.188
FMT.23: 4 residues within 4Å:- Chain B: N.707, K.710, K.711, R.714
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.711, B:R.714
- 2 x TE9: delafloxacin(Non-covalent)
TE9.24: 14 residues within 4Å:- Chain A: L.10, G.32, D.33, L.53, R.54, G.55, S.325
- Chain B: R.363
- Chain C: T.4, A.5
- Chain D: A.1, A.2
- Ligands: DT-DG-DT-DG-DG-DA-DT.1, MG.3
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain B- Hydrogen bonds: A:D.33, A:R.54, A:S.325
- Halogen bonds: A:R.54
- Water bridges: B:R.363, B:R.363
- Salt bridges: B:R.363
TE9.25: 14 residues within 4Å:- Chain A: R.363
- Chain B: L.10, G.32, D.33, L.53, R.54, G.55, S.325
- Chain C: G.1, G.2
- Chain D: C.4, G.5
- Ligands: DG-DT-DA-DA-DT-DA-DC.2, MG.15
6 PLIP interactions:1 interactions with chain A, 5 interactions with chain B- 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
- 2024-10-02
- Peptides
- DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 1 x DT- DG- DT- DG- DG- DA- DT: DNA (5'-D(TP*GP*TP*GP*GP*AP*T)-3')(Non-covalent)
- 1 x DG- DT- DA- DA- DT- DA- DC: DNA (5'-D(GP*TP*AP*AP*TP*AP*C)-3')(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 2 x MLA: MALONIC ACID(Non-covalent)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 4 x FMT: FORMIC ACID(Non-functional Binders)
- 2 x TE9: delafloxacin(Non-covalent)
- 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
- 2024-10-02
- Peptides
- DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B