› 3ejm

X-ray diffraction
1.95Å resolution

Crystal structure of the mimivirus NDK +Kpn mutant complexed with GDP

Released:
DOI: 10.2210/pdb3ejm/pdb
PDB entry 3ejm coloured by chain, front view.
PDB entry 3ejm coloured by chain, side view.
PDB entry 3ejm 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

Assemblies composition:
homo dimer (preferred)
homo hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-178386 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoside diphosphate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 146 amino acids
Theoretical weight: 16.63 KDa
Source organism: Acanthamoeba polyphaga mimivirus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5UQL3 (Residues: 2-92, 93-137; 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 GDP 2 x GDP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P63
Unit cell:
a: 70.153Å b: 70.153Å c: 104.937Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.163 0.212
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

1 mention without citation

Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Jeudy et al. (2009)