› 4eb8

X-ray diffraction
2.3Å resolution

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate

Released:
DOI: 10.2210/pdb4eb8/pdb
PDB entry 4eb8 coloured by chain, front view.
PDB entry 4eb8 coloured by chain, side view.
PDB entry 4eb8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Catalytic site conformations in human PNP by 19F-NMR and crystallography.
Suarez J, Haapalainen AM, Cahill SM, Ho MC, Yan F, Almo SC, Schramm VL
Chem Biol 20 212-22 (2013)
PMID: 23438750

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132560 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 324 amino acids
Theoretical weight: 36.13 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

3 bound ligands:
Ligand PO4 3 x PO4
Ligand IM5 3 x IM5
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 55.752Å b: 131.035Å c: 137.503Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.181 0.228
Expression system: Escherichia coli

Quick links

Citations

8 citation in other articles

Transition States and transition state analogue interactions with enzymes.
Schramm VL. (2015)
7 more

2 mentions without citation

Catalytic site conformations in human PNP by 19F-NMR and crystallography.
Suarez et al. (2013)
1 more