› 3h5q

X-ray diffraction
1.94Å resolution

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

Released:
DOI: 10.2210/pdb3h5q/pdb
PDB entry 3h5q coloured by chain, front view.
PDB entry 3h5q coloured by chain, side view.
PDB entry 3h5q coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus COL
Entry authors: Shumilin IA, Zimmerman M, Cymborowski M, Skarina T, Onopriyenko O, Anderson WF, Savchenko A, Minor W, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

Reaction catalysed: 
2'-deoxyuridine + phosphate = uracil + 2-deoxy-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177179 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrimidine-nucleoside phosphorylase Chain: A
Molecule details ›
Chain: A
Length: 436 amino acids
Theoretical weight: 47.41 KDa
Source organism: Staphylococcus aureus subsp. aureus COL
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5HE64 (Residues: 1-433; Coverage: 100%)
Gene names: SACOL2128, pdp, pyn
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand THM 1 x THM
Ligand SO4 2 x SO4
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P2
Unit cell:
a: 51.591Å b: 40.885Å c: 105.578Å
α: 90° β: 97.19° γ: 90°
R-values:
R R work R free
0.168 0.166 0.204
Expression system: Escherichia coli

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