› 7ooy

X-ray diffraction
1.9Å resolution

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 233 amino acids
Theoretical weight: 25.82 KDa
Source organism: Helicobacter pylori 26695
Expression system: Escherichia coli
UniProt:
  • Canonical: P56463 (Residues: 1-233; Coverage: 100%)
Gene names: HP_1178, deoD
Sequence domains: Phosphorylase superfamily

Ligands and Environments

4 bound ligands:
Ligand GOL 7 x GOL
Ligand TRS 1 x TRS
Ligand PO4 1 x PO4
Ligand 05Z 1 x 05Z
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P213
Unit cell:
a: 113.591Å b: 113.591Å c: 113.591Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.166 0.206
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium.
Narczyk et al. (2022)