› 5cqz

X-ray diffraction
2.9Å resolution

Human cytosolic 5'-nucleotidase II in complex with 3-(3-Imidazol-1-ylphenyl)-N-(9H-purin-6-yl)benzamide

Released:
DOI: 10.2210/pdb5cqz/pdb
PDB entry 5cqz coloured by chain, front view.
PDB entry 5cqz coloured by chain, side view.
PDB entry 5cqz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using a Fragment-Based Approach.
Marton Z, Guillon R, Krimm I, Rahimova R, Egron D, Jordheim LP, Aghajari N, Dumontet C, Périgaud C, Lionne C, Peyrottes S, Chaloin L
J Med Chem 58 9680-96 (2015)
PMID: 26599519

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156076 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic purine 5'-nucleotidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 555 amino acids
Theoretical weight: 64.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49902 (Residues: 1-536; Coverage: 96%)
Gene names: NT5B, NT5C2, NT5CP, PNT5
Sequence domains: 5' nucleotidase family

Ligands and Environments

4 bound ligands:
Ligand GOL 4 x GOL
Ligand SO4 11 x SO4
Ligand MG 4 x MG
Ligand 53O 2 x 53O
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: C2
Unit cell:
a: 143.89Å b: 121.98Å c: 90.15Å
α: 90° β: 114.29° γ: 90°
R-values:
R R work R free
0.193 0.19 0.251
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Genetics and mechanisms of NT5C2-driven chemotherapy resistance in relapsed ALL.
Dieck et al. (2019)
9 other articles