› 1k9s

X-ray diffraction
2Å resolution

PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE

Released:
DOI: 10.2210/pdb1k9s/pdb
PDB entry 1k9s coloured by chain, front view.
PDB entry 1k9s coloured by chain, side view.
PDB entry 1k9s coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism.
Koellner G, Bzowska A, Wielgus-Kutrowska B, Luić M, Steiner T, Saenger W, Stepiński J
J Mol Biol 315 351-71 (2002)
PMID: 11786017

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 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, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 237 amino acids
Theoretical weight: 25.72 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ABP8 (Residues: 2-238; Coverage: 99%)
Gene names: JW4347, b4384, deoD, pup
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand PO4 6 x PO4
Ligand FM2 3 x FM2
Ligand FM1 3 x FM1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P41212
Unit cell:
a: 178.779Å b: 178.779Å c: 167.943Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.161 0.184

Quick links

Citations

1 review citation

Enzyme Tunnels and Gates As Relevant Targets in Drug Design.
Marques et al. (2017)
35 other articles

5 mentions without citation

Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.
Štefanić et al. (2018)
4 more