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Crystal Structure of Nucleoside Kinase from Chlorobium tepidum in Complex with AMP

X-ray diffraction
1.88Å resolution
PDB entry 3kd6 coloured by chain, front view.
PDB entry 3kd6 coloured by chain, side view.
PDB entry 3kd6 coloured by chain, top view.
Source organism: Chlorobaculum tepidum
Assembly composition:
homo dimer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Carbohydrate kinase PfkB domain-containing protein
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Multimeric state: homo dimer
Accessible surface area: 22987.02 Å2
Buried surface area: 2987.47 Å2
Dissociation area: 465.69 Å2
Dissociation energy (ΔGdiss): -8.84 kcal/mol
Dissociation entropy (TΔSdiss): 12.8 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-185116
Assembly 2
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Assembly Name: Carbohydrate kinase PfkB domain-containing protein
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Multimeric state: homo dimer
Accessible surface area: 21742.39 Å2
Buried surface area: 4242.4 Å2
Dissociation area: 1,092.81 Å2
Dissociation energy (ΔGdiss): 2.96 kcal/mol
Dissociation entropy (TΔSdiss): 13.38 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-185116

Macromolecules

Carbohydrate kinase PfkB domain-containing protein
Chains: A, B
Length: 313 amino acids
Theoretical weight: 35.47 KDa
Source organism: Chlorobaculum tepidum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8KDR9 (Residues: 2-303; Coverage: 99%)
Gene name: CT0976
Pfam: pfkB family carbohydrate kinase
InterPro:
CATH: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
Carbohydrate kinase PfkB domain-containing protein in PDB entry 3kd6, assembly 1, front view.
Carbohydrate kinase PfkB domain-containing protein in PDB entry 3kd6, assembly 1, side view.
Carbohydrate kinase PfkB domain-containing protein in PDB entry 3kd6, assembly 1, top view.
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