› 2jcm

X-ray diffraction
2.15Å resolution

Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium trifluoride

Released:
DOI: 10.2210/pdb2jcm/pdb
PDB entry 2jcm coloured by chain, front view.
PDB entry 2jcm coloured by chain, side view.
PDB entry 2jcm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition.
Walldén K, Stenmark P, Nyman T, Flodin S, Gräslund S, Loppnau P, Bianchi V, Nordlund P
J Biol Chem 282 17828-36 (2007)
PMID: 17405878

Function and Biology Details

Reactions catalysed: 
A nucleotide + a 2'-deoxynriboucleoside = a nucleoside + a 2'-deoxyribonucleoside 5'-phosphate
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
IMP + H(2)O = inosine + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156075 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic purine 5'-nucleotidase Chain: A
Molecule details ›
Chain: A
Length: 555 amino acids
Theoretical weight: 64.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49902 (Residues: 1-536; Coverage: 96%)
Gene names: NT5B, NT5C2, NT5CP, PNT5
Sequence domains: 5' nucleotidase family

Ligands and Environments

3 bound ligands:
Ligand UNX 1 x UNX
Ligand MG 1 x MG
Ligand SO4 2 x SO4
1 modified residue:
Ligand BFD 1 x BFD

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I222
Unit cell:
a: 91.48Å b: 128.26Å c: 131.01Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.21 0.266
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Therapeutic potentials of ecto-nucleoside triphosphate diphosphohydrolase, ecto-nucleotide pyrophosphatase/phosphodiesterase, ecto-5'-nucleotidase, and alkaline phosphatase inhibitors.
al-Rashida et al. (2014)
4 more

1 mention without citation

Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila.
Srinivasan et al. (2014)