› 3kd6

X-ray diffraction
1.88Å resolution

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

Released:
DOI: 10.2210/pdb3kd6/pdb
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
Entry authors: Satyanarayana L, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185116 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Carbohydrate kinase PfkB domain-containing protein Chains: A, B
Molecule details ›
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
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

2 bound ligands:
Ligand AMP 2 x AMP
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 14 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 55.014Å b: 89.797Å c: 64.827Å
α: 90° β: 92.9° γ: 90°
R-values:
R R work R free
0.23 0.212 0.237
Expression system: Escherichia coli BL21(DE3)

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