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Crystal structure of the Mimivirus NDK N62L mutant complexed with dTDP

X-ray diffraction
2.6Å resolution
PDB entry 3fbf coloured by chain, front view.
PDB entry 3fbf coloured by chain, side view.
PDB entry 3fbf coloured by chain, top view.
Source organism: Acanthamoeba polyphaga mimivirus
Assembly composition:
homo hexamer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Nucleoside diphosphate kinase
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Multimeric state: homo hexamer
Accessible surface area: 31741.37 Å2
Buried surface area: 14424.78 Å2
Dissociation area: 4,894.12 Å2
Dissociation energy (ΔGdiss): -8.14 kcal/mol
Dissociation entropy (TΔSdiss): 61.6 kcal/mol
Symmetry number: 6
PDBe Complex ID: PDB-CPX-178387
Assembly 2
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Assembly Name: Nucleoside diphosphate kinase
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Multimeric state: homo hexamer
Accessible surface area: 31236.59 Å2
Buried surface area: 14669.1 Å2
Dissociation area: 5,022.94 Å2
Dissociation energy (ΔGdiss): -15.44 kcal/mol
Dissociation entropy (TΔSdiss): 61.57 kcal/mol
Symmetry number: 6
PDBe Complex ID: PDB-CPX-178387

Macromolecules

Nucleoside diphosphate kinase
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
Pfam: Nucleoside diphosphate kinase
InterPro:
CATH: Nucleoside diphosphate kinase-like domain
Nucleoside diphosphate kinase in PDB entry 3fbf, assembly 1, front view.
Nucleoside diphosphate kinase in PDB entry 3fbf, assembly 1, side view.
Nucleoside diphosphate kinase in PDB entry 3fbf, assembly 1, top view.
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