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 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDINE KINASE
A, B, C, D, E, F, G, H
195Homo sapiensMutation(s): 0 
Gene Names: TK1
EC: 2.7.1.21
Find proteins for P04183 (Homo sapiens)
Go to Gene View: TK1
Go to UniProtKB:  P04183
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DTU
Query on DTU

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

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.496α = 90.00
b = 122.920β = 130.00
c = 115.274γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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