› 9fxe

X-ray diffraction
2.12Å resolution

D204N mutant of Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine

Released:
DOI: 10.2210/pdb9fxe/pdb
PDB entry 9fxe coloured by chain, front view.
PDB entry 9fxe coloured by chain, side view.
PDB entry 9fxe coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Interaction of Tri-Cyclic Nucleobase Analogs with Enzymes of Purine Metabolism: Xanthine Oxidase and Purine Nucleoside Phosphorylase.
Stachelska-Wierzchowska A, Narczyk M, Wierzchowski J, Bzowska A, Wielgus-Kutrowska B
Int J Mol Sci 25 (2024)
PMID: 39408755

Function and Biology Details

Reaction catalysed: 
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142186 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 239 amino acids
Theoretical weight: 25.98 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ABP8 (Residues: 1-239; Coverage: 100%)
Gene names: JW4347, b4384, deoD, pup
Sequence domains: Phosphorylase superfamily

Ligands and Environments

2 bound ligands:
Ligand PO4 3 x PO4
Ligand A1IEC 3 x A1IEC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P6122
Unit cell:
a: 120.525Å b: 120.525Å c: 241.206Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.204 0.233
Expression system: Escherichia coli

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