SMTL ID : 8qmc.1

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and novel fluoroquinolone Delafloxacin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x DT- DG- DT- DG- DG- DA- DT: DNA (5'-D(*T)-R(P*G)-D(P*T)-R(P*GP*GP*A)-D(P*T)-3')(Non-covalent)

DT-DG-DT-DG-DG-DA-DT.1: 32 residues within 4Å: Chain A: E.31, G.55, K.56, D.106, 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 Chain B: Y.364 Chain C: A.5, T.6, C.7, C.8, A.9, C.10, A.11 Chain D: A.1 Ligands: MG.9, TE9.16 23 PLIP interactions: 20 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.33, A:S.34, A:N.59, A:N.59, A:G.419, A:R.481, A:R.481, A:N.572, A:N.574 Water bridges: B:R.363, B:R.363, A:K.62, A:K.62, A:K.479, A:K.479, A:K.479, A:N.570 Salt bridges: B:R.363, A:K.62, A:K.62, A:H.111, A:R.227, A:R.228 Hydrophobic interactions: A:K.56, A:I.416

1 x DG- DT- DA- DA- DT- DA- DC: DNA/RNA (5'-R(*G)-D(P*T)-R(P*AP*A)-D(P*T)-R(P*AP*C)-3')(Non-covalent)

DG-DT-DA-DA-DT-DA-DC.2: 33 residues within 4Å: Chain B: E.31, G.55, K.56, D.106, D.108, I.112, R.274, A.275, K.284, V.286, H.320, H.322, G.323, S.326, A.330, R.333, K.339, T.414, G.415, I.416, E.508, N.513, K.517 Chain C: G.1 Chain D: G.5, T.6, A.7, T.8, T.9, A.10, C.11 Ligands: MG.14, TE9.17 Protein-ligand interaction information (PLIP) not available

2 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 9 residues within 4Å: Chain A: L.624, V.627, I.628, L.668, R.672, L.673, N.675, T.676, L.681 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.675, A:N.675, A:N.675 Salt bridges: A:R.672 MLA.4: 4 residues within 4Å: Chain A: L.618, H.619, E.622, R.689 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.619 Water bridges: A:R.689 Salt bridges: A:H.619, A:R.689

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain A: G.374, Y.375, Q.378 No protein-ligand interaction detected (PLIP) ACT.6: 2 residues within 4Å: Chain A: P.443, Y.706 No protein-ligand interaction detected (PLIP)

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

MG.7: 2 residues within 4Å: Chain A: S.325 Ligands: TE9.16 No protein-ligand interaction detected (PLIP) MG.8: 6 residues within 4Å: Chain A: F.562, K.563, T.565, D.566, Q.568, I.569 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.565, A:Q.568 MG.9: 3 residues within 4Å: Chain A: D.104, D.106 Ligands: DT-DG-DT-DG-DG-DA-DT.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.104, A:D.106 MG.12: 3 residues within 4Å: Chain B: S.325 Chain C: G.1 Ligands: TE9.17 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain B: F.562, K.563, T.565, D.566, Q.568 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:F.562, B:K.563, B:T.565, B:Q.568 MG.14: 3 residues within 4Å: Chain B: D.104, D.106 Ligands: DG-DT-DA-DA-DT-DA-DC.2 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.104, B:D.106

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

CL.10: 3 residues within 4Å: Chain A: R.617, L.624, R.672 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: R.617, L.624, R.672 Ligands: MPD.11 Ligand excluded by PLIP

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

MPD.11: 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.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.624, B:L.673, B:T.676 Hydrogen bonds: B:N.675

2 x TE9: delafloxacin(Non-covalent)

TE9.16: 13 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 Ligands: DT-DG-DT-DG-DG-DA-DT.1, MG.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.10, A:D.33, A:R.54, A:R.54 Halogen bonds: A:R.54 Salt bridges: B:R.363 TE9.17: 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.12 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.363 Hydrogen bonds: B:D.33, B:D.33, B:R.54 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 (ATP-hydrolyzing),DNA topoisomerase 4 subunit A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA topoisomerase (ATP-hydrolyzing),DNA topoisomerase 4 subunit A

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