› 5fve

X-ray diffraction
2.07Å resolution

Crystal Structure of Helicobacter pylori beta clamp in complex with 3, 4-Difluorobenzamide

Released:
DOI: 10.2210/pdb5fve/pdb
Model geometry
Fit model/data
PDB entry 5fve coloured by chain, front view.
PDB entry 5fve coloured by chain, side view.
PDB entry 5fve coloured by chain, top view.
Source organism: Helicobacter pylori 26695
Primary publication:
Screening of E. coli β-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization.
Pandey P, Verma V, Dhar SK, Gourinath S
OpenAccess logo Antibiotics (Basel) 7 (2018)
PMID: 29324718

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127726 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta sliding clamp Chain: A
Molecule details ›
Chain: A
Length: 374 amino acids
Theoretical weight: 42.24 KDa
Source organism: Helicobacter pylori 26695
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O25242 (Residues: 1-374; Coverage: 100%)
Gene names: HP_0500, dnaN
Sequence domains:
Structure domains: DNA Polymerase III, subunit A, domain 2

Ligands and Environments

1 bound ligand:
Ligand 2HO 1 x 2HO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE BM14
Spacegroup: C2
Unit cell:
a: 90.071Å b: 66.383Å c: 82.778Å
α: 90° β: 115.43° γ: 90°
R-values:
R R work R free
0.214 0.213 0.247
Expression system: Escherichia coli BL21

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Citations

1 mention without citation

Screening of E. coli β-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization.
Pandey et al. (2018)