› 4jp5

X-ray diffraction
2.27Å resolution

X-ray structure of uridine phosphorylase from Yersinia pseudotuberculosis in unliganded state at 2.27 A resolution

Released:
DOI: 10.2210/pdb4jp5/pdb
Model geometry
Fit model/data
PDB entry 4jp5 coloured by chain, front view.
PDB entry 4jp5 coloured by chain, side view.
PDB entry 4jp5 coloured by chain, top view.
Source organism: Yersinia pestis
Entry authors: Balaev VV, Lashkov AA, Prokofev II, Gabdoulkhakov AG, Betzel C, Mikhailov AM

Function and Biology Details

Reaction catalysed: 
Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184037 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 253 amino acids
Theoretical weight: 27.12 KDa
Source organism: Yersinia pestis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8D1I4 (Residues: 16-268; Coverage: 94%)
Gene names: YP_3263, udp, y0444
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand EDO 3 x EDO
Ligand SO4 1 x SO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
Spacegroup: P32
Unit cell:
a: 93.75Å b: 93.75Å c: 146.58Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.178 0.202
Expression system: Escherichia coli

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