› 2dy9

X-ray diffraction
2.01Å resolution

Crystal structure of nucleoside diphosphate kinase in complex with ADP

Released:
DOI: 10.2210/pdb2dy9/pdb
PDB entry 2dy9 coloured by chain, front view.
PDB entry 2dy9 coloured by chain, side view.
PDB entry 2dy9 coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Entry authors: Kato-Murayama M, Murayama K, Terada T, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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-129724 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 160 amino acids
Theoretical weight: 18.34 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58429 (Residues: 1-157; Coverage: 100%)
Gene names: PH0698, ndk
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand CL 4 x CL
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P63
Unit cell:
a: 69.835Å b: 69.835Å c: 106.897Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.122 0.122 0.168
Expression system: Escherichia coli

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