› 4mch

X-ray diffraction
1.73Å resolution

Crystal structure of uridine phosphorylase from vibrio fischeri es114 complexed with 6-hydroxy-1-naphthoic acid, NYSGRC Target 029520.

Released:
DOI: 10.2210/pdb4mch/pdb
PDB entry 4mch coloured by chain, front view.
PDB entry 4mch coloured by chain, side view.
PDB entry 4mch coloured by chain, top view.
Source organism: Aliivibrio fischeri ES114
Entry authors: Malashkevich VN, Bhosle R, Toro R, Hillerich B, Gizzi A, Garforth S, Kar A, Chan MK, Lafluer J, Patel H, Matikainen B, Chamala S, Lim S, Celikgil A, Villegas G, Evans B, Love J, Fiser A, Khafizov K, Seidel R, Bonanno JB, Almo SC, New York Structural Genomics Research Consortium (NYSGRC)

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-176992 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chain: A
Molecule details ›
Chain: A
Length: 266 amino acids
Theoretical weight: 29.83 KDa
Source organism: Aliivibrio fischeri ES114
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5E046 (Residues: 1-244; Coverage: 100%)
Gene name: VF_A0530
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand 61N 1 x 61N
Ligand DMS 14 x DMS
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: R32
Unit cell:
a: 163.975Å b: 163.975Å c: 58.355Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.174 0.173 0.196
Expression system: Escherichia coli BL21(DE3)

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