› 4ts9

X-ray diffraction
1.77Å resolution

Crystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC molecules

Released:
DOI: 10.2210/pdb4ts9/pdb
PDB 4ts9 coloured by chain and viewed from the front.
PDB 4ts9 coloured by chain and viewed from the side.
PDB 4ts9 coloured by chain and viewed from the top.
Source organism: Escherichia coli
Primary publication:
Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.
Štefanić Z, Narczyk M, Mikleušević G, Kazazić S, Bzowska A, Luić M
Sci Rep 8 15427 (2018)
PMID: 30337572

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)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 237 amino acids
Theoretical weight: 25.74 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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6122
Unit cell:
a: 120.625Å b: 120.625Å c: 240.006Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.157 0.156 0.177

Quick links

Citations

2 citation in other articles

A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit.
Medvedev et al. (2021)
1 more

4 mentions without citation

Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases.
Il'icheva et al. (2020)
3 more