› 5opm

X-ray diffraction
1.68Å resolution

Crystal structure of D52N/R238W cN-II mutant bound to dATP and free phosphate

Released:
DOI: 10.2210/pdb5opm/pdb
PDB entry 5opm coloured by chain, front view.
PDB entry 5opm coloured by chain, side view.
PDB entry 5opm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation.
Hnízda A, Fábry M, Moriyama T, Pachl P, Kugler M, Brinsa V, Ascher DB, Carroll WL, Novák P, Žaliová M, Trka J, Řezáčová P, Yang JJ, Veverka V
Leukemia 32 1393-1403 (2018)
PMID: 29535428

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
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 Chain: A
Molecule details ›
Chain: A
Length: 478 amino acids
Theoretical weight: 55.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49902 (Residues: 3-488; Coverage: 85%)
Gene names: NT5B, NT5C2, NT5CP, PNT5
Sequence domains: 5' nucleotidase family

Ligands and Environments

4 bound ligands:
Ligand PO4 1 x PO4
Ligand MG 2 x MG
Ligand DTP 1 x DTP
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: I222
Unit cell:
a: 92.087Å b: 127.454Å c: 130.948Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.178 0.197
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Nucleobase and Nucleoside Analogues: Resistance and Re-Sensitisation at the Level of Pharmacokinetics, Pharmacodynamics and Metabolism.
Tsesmetzis et al. (2018)
3 more