› 1pae

X-ray diffraction
2.7Å resolution

nucleoside diphosphate kinase

Released:
DOI: 10.2210/pdb1pae/pdb
PDB entry 1pae coloured by chain, front view.
PDB entry 1pae coloured by chain, side view.
PDB entry 1pae coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing.
Strub MP, Hoh F, Sanchez JF, Strub JM, Böck A, Aumelas A, Dumas C
Structure 11 1359-67 (2003)
PMID: 14604526

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: X
Molecule details ›
Chain: X
Length: 155 amino acids
Theoretical weight: 16.97 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 SE 2 x SE
1 modified residue:
Ligand MSE 3 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: LURE BEAMLINE DW32
Spacegroup: P6322
Unit cell:
a: 76.633Å b: 76.633Å c: 106.51Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.182 0.232
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Discovery, synthesis, and structure-activity relationships of conotoxins.
Akondi et al. (2014)
6 more