› 5m2t

X-ray diffraction
1.03Å resolution

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution

Released:
DOI: 10.2210/pdb5m2t/pdb
PDB entry 5m2t coloured by chain, front view.
PDB entry 5m2t coloured by chain, side view.
PDB entry 5m2t coloured by chain, top view.
Source organism: Vibrio cholerae
Entry authors: Prokofev II, Lashkov AA, Gabdulkhakov 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, udp, udp_1
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

5 bound ligands:
Ligand URI 6 x URI
Ligand NA 3 x NA
Ligand CL 6 x CL
Ligand MG 1 x MG
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P1
Unit cell:
a: 64.323Å b: 72.039Å c: 89.193Å
α: 110.56° β: 107.53° γ: 85.83°
R-values:
R R work R free
0.118 0.118 0.137
Expression system: Escherichia coli

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