› 5epu

X-ray diffraction
1.06Å resolution

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.

Released:
DOI: 10.2210/pdb5epu/pdb
PDB entry 5epu coloured by chain, front view.
PDB entry 5epu coloured by chain, side view.
PDB entry 5epu coloured by chain, top view.
Source organism: Vibrio cholerae
Entry authors: Prokofev II, Lashkov AA, 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-191760 (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: 27.11 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9K4U1 (Residues: 1-253; Coverage: 100%)
Gene names: BC353_05040, D6U24_08385, ERS013201_00032, EYB64_00255, F0M16_20765, FLM02_10845, FLM12_04550, QXB71_001489, udp, udp_1
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

7 bound ligands:
Ligand CYT 6 x CYT
Ligand GOL 6 x GOL
Ligand MG 7 x MG
Ligand NA 3 x NA
Ligand CL 2 x CL
Ligand TRS 2 x TRS
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 92.848Å b: 96.715Å c: 92.89Å
α: 90° β: 119.96° γ: 90°
R-values:
R R work R free
0.106 0.105 0.122
Expression system: Escherichia coli

Quick links