› 4uof

X-ray diffraction
2.1Å resolution

Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dADP

Released:
DOI: 10.2210/pdb4uof/pdb
PDB entry 4uof coloured by chain, front view.
PDB entry 4uof coloured by chain, side view.
PDB entry 4uof coloured by chain, top view.
Source organism: Penaeus vannamei
Primary publication:
Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates.
López-Zavala AA, Quintero-Reyes IE, Carrasco-Miranda JS, Stojanoff V, Weichsel A, Rudiño-Piñera E, Sotelo-Mundo RR
Acta Crystallogr F Struct Biol Commun 70 1150-4 (2014)
PMID: 25195883

Function and Biology Details

Reaction catalysed: 
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107639 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 151 amino acids
Theoretical weight: 17.02 KDa
Source organism: Penaeus vannamei
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: A5J299 (Residues: 1-151; Coverage: 100%)
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

2 bound ligands:
Ligand DAT 3 x DAT
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: C2221
Unit cell:
a: 70.11Å b: 134.38Å c: 104.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.19 0.249
Expression system: Escherichia coli BL21

Quick links

Citations

3 citation in other articles

Pyrrole-indolinone SU11652 targets the nucleoside diphosphate kinase from Leishmania parasites.
Vieira et al. (2017)
2 more

1 mention without citation

Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates.
López-Zavala et al. (2014)