› 6rca

X-ray diffraction
1.34Å resolution

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 2.2'-anhydrouridine at 1.34 A

Released:
DOI: 10.2210/pdb6rca/pdb
PDB entry 6rca coloured by chain, front view.
PDB entry 6rca coloured by chain, side view.
PDB entry 6rca coloured by chain, top view.
Source organism: Vibrio cholerae
Primary publication:
X-Ray Structure and Molecular Dynamics Study of Uridine Phosphorylase from Vibrio cholerae in Complex with 2,2'-Anhydrouridine
Eistrikh-Geller PA, Rubinsky SV, Prokofev II, Gabdoulkhakov AG, Mironov AS, Lashkov AA
Crystallography Reports (2020)

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, KIN13_10845, udp, udp_1
Sequence domains: Phosphorylase superfamily

Ligands and Environments

6 bound ligands:
Ligand NA 3 x NA
Ligand BJE 6 x BJE
Ligand GOL 8 x GOL
Ligand CL 2 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: P31
Unit cell:
a: 93.245Å b: 93.245Å c: 152.928Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.136 0.135 0.169
Expression system: Escherichia coli

Quick links