› 1ndc

X-ray diffraction
2Å resolution

X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION

Released:
DOI: 10.2210/pdb1ndc/pdb
PDB entry 1ndc coloured by chain, front view.
PDB entry 1ndc coloured by chain, side view.
PDB entry 1ndc coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
X-ray structure of nucleoside diphosphate kinase complexed with thymidine diphosphate and Mg2+ at 2-A resolution.
Cherfils J, Moréra S, Lascu I, Véron M, Janin J
Biochemistry 33 9062-9 (1994)
PMID: 8049207

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 Chain: A
Molecule details ›
Chain: A
Length: 155 amino acids
Theoretical weight: 16.82 KDa
Source organism: Dictyostelium discoideum
Expression system: Not provided
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

2 bound ligands:
Ligand MG 1 x MG
Ligand TYD 1 x TYD
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: R32
Unit cell:
a: 79.8Å b: 79.8Å c: 160.6Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.183 not available
Expression system: Not provided

Quick links

Citations

7 review citations

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

1 mention without citation

Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Jeudy et al. (2009)