› 1bux

X-ray diffraction
2.8Å resolution

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Released:
DOI: 10.2210/pdb1bux/pdb
PDB entry 1bux coloured by chain, front view.
PDB entry 1bux coloured by chain, side view.
PDB entry 1bux coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.
Schneider B, Xu YW, Janin J, Véron M, Deville-Bonne D
J Biol Chem 273 28773-8 (1998)
PMID: 9786875

Function and Biology Details

Reaction catalysed: 
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149819 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase, cytosolic Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 155 amino acids
Theoretical weight: 16.82 KDa
Source organism: Dictyostelium discoideum
Expression system: Escherichia coli
UniProt:
  • Canonical: P22887 (Residues: 1-155; Coverage: 100%)
Gene names: DDB_G0273069, DDB_G0273805, gip17, ndkB, ndkC-1, ndkC-2
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

1 bound ligand:
Ligand PPS 3 x PPS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P3121
Unit cell:
a: 71.5Å b: 71.5Å c: 153.9Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.204 0.312
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The catalytic mechanism of nucleoside diphosphate kinases.
Lascu et al. (2000)
2 more

2 mentions without citation

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.
Kikuchi et al. (2011)
1 more