2QRN

Human Deoxycytidine kinase dCMP, UDP, Mg ion product complex

• PDB DOI: https://doi.org/10.2210/pdb2QRN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-28 Released: 2007-12-11 
• Deposition Author(s): Ealick, S.E., Soriano, E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

Structures of human deoxycytidine kinase product complexes.

Soriano, E.V., Clark, V.C., Ealick, S.E.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1201-1207

• PubMed: 18084067 
• DOI: https://doi.org/10.1107/S0907444907048834
• Primary Citation of Related Structures:  
  2QRN, 2QRO


• PubMed Abstract: 
  

  Human deoxycytidine kinase (dCK) is involved in the nucleotide-biosynthesis salvage pathway and has also been shown to phosphorylate several antitumor and antiviral prodrugs. The structures of dCK alone and the dead-end complex of dCK with substrate nucleoside and product ADP or UDP have previously been reported; however, there is currently no structure available for a substrate or product complex. Here, the structures of dCK complexes with the products dCMP, UDP and Mg2+ ion, and with dAMP, UDP and Mg2+ ion are reported. Structural comparisons show that the product complexes with UDP and a dead-end complex with substrate and UDP have similar active-site conformations.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 133.84 kDa 
• Atom Count: 7,808 
• Modelled Residue Count: 912 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxycytidine kinase	A, B, C, D	280	Homo sapiens	Mutation(s): 0  Gene Names: DCK EC: 2.7.1.74 (PDB Primary Data), 2.7.1.113 (UniProt), 2.7.1.76 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens) Explore P27707  Go to UniProtKB:  P27707
PHAROS:  P27707 GTEx:  ENSG00000156136

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	F [auth A], I [auth B], L [auth C], O [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
DCM	G [auth A], J [auth B], M [auth C], P [auth D]	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O7 P NCMVOABPESMRCP-SHYZEUOFSA-N
MG	E [auth A], H [auth B], K [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.565	α = 90
b = 94.565	β = 90
c = 335.334	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Ealick, S.E., Soriano, E.V.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description