› 4hz0

X-ray diffraction
2.2Å resolution

Pyrrolopyrimidine inhibitors of dna gyrase b and topoisomerase iv, part i: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.

Released:
DOI: 10.2210/pdb4hz0/pdb
PDB entry 4hz0 coloured by chain, front view.
PDB entry 4hz0 coloured by chain, side view.
PDB entry 4hz0 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.
Tari LW, Trzoss M, Bensen DC, Li X, Chen Z, Lam T, Zhang J, Creighton CJ, Cunningham ML, Kwan B, Stidham M, Shaw KJ, Lightstone FC, Wong SE, Nguyen TB, Nix J, Finn J
Bioorg Med Chem Lett 23 1529-36 (2013)
PMID: 23352267

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148844 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA topoisomerase 4 subunit B Chains: A, B
Molecule details ›
Chains: A, B
Length: 213 amino acids
Theoretical weight: 23.86 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20083 (Residues: 12-216; Coverage: 33%)
Gene names: JW2998, b3030, nfxD, parE
Sequence domains: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
Structure domains: Histidine kinase-like ATPase, C-terminal domain

Ligands and Environments

2 bound ligands:
Ligand 1AV 2 x 1AV
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P21
Unit cell:
a: 52.166Å b: 50.064Å c: 85.812Å
α: 90° β: 94.72° γ: 90°
R-values:
R R work R free
0.311 0.213 0.286
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Targeting DNA Replication and Repair for the Development of Novel Therapeutics against Tuberculosis.
Reiche et al. (2017)
4 more

1 mention without citation

Antimicrobial Activity and Molecular Docking Studies of the Biotransformation of Diterpene Acanthoic Acid Using the Fungus Xylaria sp.
Marinho et al. (2023)