SMTL ID : 8qmb.1

Nucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin

Coordinates

PDB Format Compare

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)

DT-DG-DT-DG-DG-DA-DT.1: 30 residues within 4Å: Chain A: 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.325, S.326, A.330, R.333, K.339, T.414, I.416, E.508 Chain C: A.5, T.6, C.7, C.8, A.9, C.10, A.11 Chain D: A.1 Ligands: MG.5, TE9.24 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.33, A:S.34, A:A.35, A:R.54, A:R.54, A:N.59, A:N.59, A:G.419, A:R.481, A:N.572 Water bridges: B:R.363, A:K.62, A:K.62, A:R.228, A:R.228, A:Y.266, A:K.479, A:K.479, A:N.574 Hydrophobic interactions: A:V.224, A:I.416 Salt bridges: A:K.62, A:K.62, A:H.111, A:R.227, A:R.228

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)

CL.6: 3 residues within 4Å: Chain A: R.617, L.624, R.672 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: R.617, L.624, R.672 Ligands: MPD.22 Ligand excluded by PLIP

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
A

B
B

DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A

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