› 3of3

X-ray diffraction
1.83Å resolution

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

Released:
DOI: 10.2210/pdb3of3/pdb
PDB entry 3of3 coloured by chain, front view.
PDB entry 3of3 coloured by chain, side view.
PDB entry 3of3 coloured by chain, top view.
Source organism: Vibrio cholerae
Entry authors: Kim J, Ramagopal UA, Burley SK, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-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-192010 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type 1 Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 241 amino acids
Theoretical weight: 26.15 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KPM0 (Residues: 1-241; Coverage: 100%)
Gene names: VC_2347, deoD1
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand DIH 12 x DIH
Ligand PO4 12 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 101.375Å b: 160.974Å c: 188.685Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.188
Expression system: Escherichia coli BL21(DE3)

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