› 1kdn

X-ray diffraction
2Å resolution

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE

Released:
DOI: 10.2210/pdb1kdn/pdb
PDB entry 1kdn coloured by chain, front view.
PDB entry 1kdn coloured by chain, side view.
PDB entry 1kdn coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.
Xu YW, Moréra S, Janin J, Cherfils J
Proc Natl Acad Sci U S A 94 3579-83 (1997)
PMID: 9108019

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

3 bound ligands:
Ligand MG 3 x MG
Ligand AF3 3 x AF3
Ligand ADP 3 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LURE BEAMLINE DW32
Spacegroup: P3121
Unit cell:
a: 71.354Å b: 71.354Å c: 153.494Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.177 0.177 0.179
Expression system: Escherichia coli

Quick links

Citations

16 review citations

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

4 mentions without citation

AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.
Xu et al. (1997)
3 more