1P7C

Crystal Structure of HSV1-TK complexed with TP5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases.

Gardberg, A.Shuvalova, L.Monnerjahn, C.Konrad, M.Lavie, A.

(2003) Structure 11: 1265-1277

  • DOI: 10.1016/j.str.2003.09.003
  • Primary Citation of Related Structures:  
    1P75, 1P73, 1P72, 1P6X, 1P7C

  • PubMed Abstract: 
  • Crystal structures of equine herpesvirus type-4 thymidine kinase (EHV4-TK) in complex with (i). thymidine and ADP, (ii). thymidine and SO(4) and the bisubstrate analogs, (iii). TP(4)A, and (iv). TP(5)A have been solved. Additionally, the structure of ...

    Crystal structures of equine herpesvirus type-4 thymidine kinase (EHV4-TK) in complex with (i). thymidine and ADP, (ii). thymidine and SO(4) and the bisubstrate analogs, (iii). TP(4)A, and (iv). TP(5)A have been solved. Additionally, the structure of herpes simplex virus type-1 thymidine kinase (HSV1-TK) in complex with TP(5)A has been determined. These are the first structures of nucleoside kinases revealing conformational transitions upon binding of bisubstrate analogs. The structural basis for the dual thymidine and thymidylate kinase activity of these TKs is elucidated. While the active sites of HSV1-TK and EHV4-TK resemble one another, notable differences are observed in the Lid regions and in the way the enzymes bind the base of the phosphoryl-acceptor. The latter difference could partly explain the higher activity of EHV4-TK toward the prodrug ganciclovir.


    Organizational Affiliation

    University of Illinois at Chicago, Department of Biochemistry and Molecular Biology, 1819 West Polk St, Chicago, IL 60612, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidine kinaseAB343Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: TK OR UL23TKUL23
EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17))
Explore P03176 
Go to UniProtKB:  P03176
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T5A
Query on T5A

Download Ideal Coordinates CCD File 
A
P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
C20 H30 N7 O23 P5
JCFDSPQTEMXXLO-SLFMBYJQSA-N
 Ligand Interaction
THM
Query on THM

Download Ideal Coordinates CCD File 
B
THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
THMΔG:  29.81999969482422   kJ/mol  BindingDB
THM-TΔS:  50.09000015258789   kJ/mol  BindingDB
THM-TΔS:  36.880001068115234   kJ/mol  BindingDB
THM-TΔS:  42.79999923706055   kJ/mol  BindingDB
THMΔG:  30.239999771118164   kJ/mol  BindingDB
THMΔH:  73.08000183105469   kJ/mol  BindingDB
THMIC50:  1000   nM  BindingDB
THMΔH:  79.91000366210938   kJ/mol  BindingDB
THMΔH:  57.119998931884766   kJ/mol  BindingDB
THM-TΔS:  27.18000030517578   kJ/mol  BindingDB
THMΔG:  29.399999618530273   kJ/mol  BindingDB
THMΔH:  66.36000061035156   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.244 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.219α = 90
b = 117.847β = 90
c = 108.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance