› 1b4s

X-ray diffraction
2.5Å resolution

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT

Released:
DOI: 10.2210/pdb1b4s/pdb
PDB entry 1b4s coloured by chain, front view.
PDB entry 1b4s coloured by chain, side view.
PDB entry 1b4s coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
Admiraal SJ, Schneider B, Meyer P, Janin J, Véron M, Deville-Bonne D, Herschlag D
Biochemistry 38 4701-11 (1999)
PMID: 10200157

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: 16.74 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 PO4 3 x PO4
Ligand MG 3 x MG
Ligand ADP 3 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LURE BEAMLINE D41A
Spacegroup: P3121
Unit cell:
a: 70Å b: 70Å c: 151.77Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.203 0.203 0.305
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis.
Lassila et al. (2011)
10 more

1 mention without citation

Relating destabilizing regions to known functional sites in proteins.
Dessailly et al. (2007)