› 3bgs

X-ray diffraction
2.1Å resolution

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate

Released:
DOI: 10.2210/pdb3bgs/pdb
PDB entry 3bgs coloured by chain, front view.
PDB entry 3bgs coloured by chain, side view.
PDB entry 3bgs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.
Rinaldo-Matthis A, Murkin AS, Ramagopal UA, Clinch K, Mee SP, Evans GB, Tyler PC, Furneaux RH, Almo SC, Schramm VL
J Am Chem Soc 130 842-4 (2008)
PMID: 18154341

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 domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132560 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase Chain: A
Molecule details ›
Chain: A
Length: 289 amino acids
Theoretical weight: 32.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00491 (Residues: 1-289; Coverage: 100%)
Gene names: NP, PNP
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand PO4 3 x PO4
Ligand DIH 1 x DIH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: R32
Unit cell:
a: 142.801Å b: 142.801Å c: 167.348Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.219 0.218 0.249
Expression system: Escherichia coli

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Citations

1 review citation

From crystal to compound: structure-based antimalarial drug discovery.
Drinkwater et al. (2014)
8 other articles

9 mentions without citation

Enzymatic Transition States and Drug Design.
Schramm VL. (2018)
8 more