› 5miw

X-ray diffraction
1.28Å resolution

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uracil at 1.28 A.

Released:
DOI: 10.2210/pdb5miw/pdb
PDB entry 5miw coloured by chain, front view.
PDB entry 5miw coloured by chain, side view.
PDB entry 5miw coloured by chain, top view.
Source organism: Vibrio cholerae
Entry authors: Prokofev II, Lashkov AA, Balaev VV, 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, udp, udp_1
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

6 bound ligands:
Ligand CL 8 x CL
Ligand NA 6 x NA
Ligand URA 6 x URA
Ligand SO4 2 x SO4
Ligand GOL 10 x GOL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.3
Spacegroup: P1
Unit cell:
a: 64.513Å b: 71.948Å c: 89.332Å
α: 69.22° β: 72.2° γ: 85.6°
R-values:
R R work R free
0.133 0.132 0.169
Expression system: Escherichia coli

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