› 7op9

X-ray diffraction
1.5Å resolution

Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 2,6-dichloropurine

Released:
DOI: 10.2210/pdb7op9/pdb
Model geometry
Fit model/data
PDB entry 7op9 coloured by chain, front view.
PDB entry 7op9 coloured by chain, side view.
PDB entry 7op9 coloured by chain, top view.
Source organism: Helicobacter pylori 26695
Primary publication:
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 M, Wojtyś MI, Leščić Ašler I, Žinić B, Luić M, Jagusztyn-Krynicka EK, Štefanić Z, Bzowska A
OpenAccess logo J Enzyme Inhib Med Chem 37 1083-1097 (2022)
PMID: 35437103

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, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 233 amino acids
Theoretical weight: 25.87 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

3 bound ligands:
Ligand 06K 12 x 06K
Ligand IMD 13 x IMD
Ligand MG 12 x MG
1 modified residue:
Ligand OCS 12 x OCS

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P1
Unit cell:
a: 93.419Å b: 93.428Å c: 95.459Å
α: 81.91° β: 79.35° γ: 60.09°
R-values:
R R work R free
0.173 0.173 0.196
Expression system: Escherichia coli

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Citations

2 mentions without citation

Sequetyping: serotyping Streptococcus pneumoniae by a single PCR sequencing strategy.
Leung et al. (2012)
1 more

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