2QRN

Human Deoxycytidine kinase dCMP, UDP, Mg ion product complex

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 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxycytidine kinase
A, B, C, D
280Homo sapiensMutation(s): 0 
Gene Names: DCK
EC: 2.7.1.74
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens)
Explore P27707 
Go to UniProtKB:  P27707
PHAROS:  P27707
GTEx:  ENSG00000156136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27707
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]		URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
DCM
Query on DCM
Download Ideal Coordinates CCD File 
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
Query on MG
Download Ideal Coordinates CCD File 
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 = 94.565α = 90
b = 94.565β = 90
c = 335.334γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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