1W4R

Structure of a type II thymidine kinase with bound dTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a Type II Thymidine Kinase with Bound Dttp

Birringer, M.S.Claus, M.T.Folkers, G.Kloer, D.P.Schulz, G.E.Scapozza, L.

(2005) FEBS Lett 579: 1376

  • DOI: 10.1016/j.febslet.2005.01.034
  • Primary Citation of Related Structures:  
    1W4R

  • PubMed Abstract: 
  • The structure of human cytosolic thymidine kinase in complex with its feedback inhibitor 2'-deoxythymidine-5'-triphosphate was determined. This structure is the first representative of the type II thymidine kinases found in several pathogens. The str ...

    The structure of human cytosolic thymidine kinase in complex with its feedback inhibitor 2'-deoxythymidine-5'-triphosphate was determined. This structure is the first representative of the type II thymidine kinases found in several pathogens. The structure deviates strongly from the known structures of type I thymidine kinases such as the Herpes simplex enzyme. It contains a zinc-binding domain with four cysteines complexing a structural zinc ion. Interestingly, the backbone atoms of the type II enzyme bind thymine via hydrogen-bonds, in contrast to type I, where side chains are involved. This results in a specificity difference exploited for antiviral therapy. The presented structure will foster the development of new drugs and prodrugs for numerous therapeutic applications.


    Organizational Affiliation

    Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Wolfgang-Pauli Strasse 10, 8093 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDINE KINASEA, B, C, D, E, F, G, H195Homo sapiensMutation(s): 0 
Gene Names: TK1
EC: 2.7.1.21
Find proteins for P04183 (Homo sapiens)
Explore P04183 
Go to UniProtKB:  P04183
NIH Common Fund Data Resources
PHAROS  P04183
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download CCD File 
A, B, C, D, E, F, G, H
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
DTU
Query on DTU

Download CCD File 
E
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-ZXZARUISSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.496α = 90
b = 122.92β = 130
c = 115.274γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance