Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75640.86 
• Atom Count: 4731 
• Residue Count: 686 
• Unique protein chains: 1

1P7C

Crystal Structure of HSV1-TK complexed with TP5A

• DOI: 10.2210/pdb1P7C/pdb

• Classification: TRANSFERASE
• Organism(s): Human herpesvirus 1 (strain 17)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-05-01 Released: 2003-11-04 
• Deposition Author(s): Gardberg, A., Shuvalova, L., Monnerjahn, C., Konrad, M., Lavie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.285 
• R-Value Work: 0.239 

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

• PubMed: 14527394 
• Primary Citation of Related Structures:  
  1P75, 1P73, 1P72, 1P6X


• 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 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.

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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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thymidine kinase	A, B	343	Human herpesvirus 1 (strain 17)	Mutation(s): 0  Gene Names: TK EC: 2.7.1.21
Find proteins for P03176 (Human herpesvirus 1 (strain 17)) Go to UniProtKB:  P03176

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
THM	B	THYMIDINE DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
T5A	A	P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE C20 H30 N7 O23 P5 JCFDSPQTEMXXLO-SLFMBYJQSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
THM	IC50: 1000 nM (99) BINDINGDB
THM	ΔH: -57.1 - -79.9 kJ/mol (100) BINDINGDB
THM	ΔG: -29.4 - -30.2 kJ/mol (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.285 
• R-Value Work: 0.239 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 113.219	α = 90.00
b = 117.847	β = 90.00
c = 108.400	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-01 
• Released Date: 2003-11-04 
• Deposition Author(s): Gardberg, A., Shuvalova, L., Monnerjahn, C., Konrad, M., Lavie, A.

Revision History 

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