› 3eic

X-ray diffraction
2.3Å resolution

X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP

Released:
DOI: 10.2210/pdb3eic/pdb
PDB entry 3eic coloured by chain, front view.
PDB entry 3eic coloured by chain, side view.
PDB entry 3eic coloured by chain, top view.
Source organism: Acanthamoeba polyphaga mimivirus
Primary publication:
Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Jeudy S, Lartigue A, Claverie JM, Abergel C
J Virol 83 7142-50 (2009)
PMID: 19439473

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178387 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 142 amino acids
Theoretical weight: 16.3 KDa
Source organism: Acanthamoeba polyphaga mimivirus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5UQL3 (Residues: 2-137; Coverage: 99%)
Gene names: MIMI_R418, NDK
Sequence domains: Nucleoside diphosphate kinase
Structure domains: Nucleoside diphosphate kinase-like domain

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand UDP 6 x UDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2221
Unit cell:
a: 80.472Å b: 152.726Å c: 184.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.224
Expression system: Escherichia coli

Quick links

Citations

5 review citations

The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus.
Abergel et al. (2015)
4 more

3 mentions without citation

Kinases as targets for chemical modulators: Structural aspects and their role in spermatogenesis.
Jenardhanan et al. (2014)
2 more