› 5mx8

X-ray diffraction
2.4Å resolution

Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-3

Released:
DOI: 10.2210/pdb5mx8/pdb
PDB entry 5mx8 coloured by chain, front view.
PDB entry 5mx8 coloured by chain, side view.
PDB entry 5mx8 coloured by chain, top view.
Source organism: Helicobacter pylori
Primary publication:
Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori.
Štefanić Z, Mikleušević G, Luić M, Bzowska A, Leščić Ašler I
Int J Biol Macromol 101 518-526 (2017)
PMID: 28336275

Function and Biology Details

Reaction catalysed: 
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157474 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 25.82 KDa
Source organism: Helicobacter pylori
UniProt:
  • Canonical: P56463 (Residues: 1-233; Coverage: 100%)
Gene names: HP_1178, deoD
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand HPA 1 x HPA
Ligand PO4 1 x PO4
Ligand PG4 8 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: OXFORD DIFFRACTION ENHANCE ULTRA
Spacegroup: P4132
Unit cell:
a: 143.596Å b: 143.596Å c: 143.596Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.214 0.259

Quick links

Citations

1 review citation

Helicobacter pylori treatment in the post-antibiotics era-searching for new drug targets.
Roszczenko-Jasińska et al. (2020)
5 other articles