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


Ligand Structure Quality Assessment 


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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDINE KINASE
A, B, C, D, E
A, B, C, D, E, F, G, H
195Homo sapiensMutation(s): 0 
EC: 2.7.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P04183 (Homo sapiens)
Explore P04183 
Go to UniProtKB:  P04183
PHAROS:  P04183
GTEx:  ENSG00000167900 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04183
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
T [auth F],
V [auth G],
X [auth H]
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
DTU
Query on DTU

Download Ideal Coordinates CCD File 
S [auth E](2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-ZXZARUISSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
U [auth F],
W [auth G],
Y [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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