› 2zia

X-ray diffraction
1.8Å resolution

C4S dCK variant of dCK in complex with cladribine+UDP

Released:
DOI: 10.2210/pdb2zia/pdb
PDB entry 2zia coloured by chain, front view.
PDB entry 2zia coloured by chain, side view.
PDB entry 2zia coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase.
Sabini E, Hazra S, Konrad M, Lavie A
J Med Chem 51 4219-25 (2008)
PMID: 18570408

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
Molecule details ›
Chains: A, B
Length: 279 amino acids
Theoretical weight: 32.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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 2 x UDP
Ligand CL9 2 x CL9
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 67.76Å b: 44.09Å c: 94.64Å
α: 90° β: 95.71° γ: 90°
R-values:
R R work R free
0.207 0.202 0.25
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Highlights in Resistance Mechanism Pathways for Combination Therapy.
Delou et al. (2019)
5 other articles

3 mentions without citation

Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release.
Hazra et al. (2011)
2 more