› 2zi6

X-ray diffraction
1.77Å resolution

C4S dCK variant of dCK in complex with D-dA+UDP

Released:
DOI: 10.2210/pdb2zi6/pdb
PDB entry 2zi6 coloured by chain, front view.
PDB entry 2zi6 coloured by chain, side view.
PDB entry 2zi6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for substrate promiscuity of dCK.
Sabini E, Hazra S, Ort S, Konrad M, Lavie A
J Mol Biol 378 607-21 (2008)
PMID: 18377927

Function and Biology Details

Reactions catalysed: 
ATP + deoxyguanosine = ADP + dGMP
NTP + deoxycytidine = NDP + dCMP
ATP + deoxyadenosine = ADP + dAMP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151058 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxycytidine kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 279 amino acids
Theoretical weight: 32.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P27707 (Residues: 1-260; Coverage: 100%)
Gene name: DCK
Sequence domains: Deoxynucleoside kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand UDP 4 x UDP
Ligand 3D1 4 x 3D1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2221
Unit cell:
a: 138.25Å b: 138.51Å c: 118.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.283
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I.
Padavannil et al. (2021)
1 more

3 mentions without citation

Structural basis for substrate promiscuity of dCK.
Sabini et al. (2008)
2 more