› 5eix

X-ray diffraction
3.35Å resolution

QUINOLONE-STABILIZED CLEAVAGE COMPLEX OF TOPOISOMERASE IV FROM KLEBSIELLA PNEUMONIAE

Released:
DOI: 10.2210/pdb5eix/pdb
PDB entry 5eix coloured by chain, front view.
PDB entry 5eix coloured by chain, side view.
PDB entry 5eix coloured by chain, top view.
Source organism: Klebsiella pneumoniae subsp. rhinoscleromatis SB3432
Primary publication:
Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex.
Veselkov DA, Laponogov I, Pan XS, Selvarajah J, Skamrova GB, Branstrom A, Narasimhan J, Prasad JV, Fisher LM, Sanderson MR
Acta Crystallogr D Struct Biol 72 488-96 (2016)
PMID: 27050128

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118636 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase 4 subunit A; DNA topoisomerase 4 subunit B Chains: A, B, G, J
Molecule details ›
Chains: A, B, G, J
Length: 741 amino acids
Theoretical weight: 83.92 KDa
Source organism: Klebsiella pneumoniae subsp. rhinoscleromatis SB3432
Expression system: Escherichia coli
UniProt:
  • Canonical: R4YHS8 (Residues: 390-631; Coverage: 38%)
  • Canonical: R4YE07 (Residues: 1-490; Coverage: 65%)
Gene names: KPR_4469, KPR_4476, parC, parE
Sequence domains:
Structure domains: Rossmann fold
SYMMETRISED E-SITE (PRE-CUT) Chains: C, E, H, K
Molecule details ›
Chains: C, E, H, K
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
SYMMETRISED E-SITE (PRE-CUT) Chains: D, F, I, L
Molecule details ›
Chains: D, F, I, L
Length: 12 nucleotides
Theoretical weight: 3.66 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 8 x MG
Ligand LFX 4 x LFX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 102.07Å b: 161.53Å c: 138.6Å
α: 90° β: 94.22° γ: 90°
R-values:
R R work R free
0.226 0.224 0.259
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Topoisomerases as anticancer targets.
Delgado et al. (2018)
4 other articles

6 mentions without citation

Two Decades of Successful SAR-Grounded Stories of the Novel Bacterial Topoisomerase Inhibitors (NBTIs).
Kolarič et al. (2020)
5 more