Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 75.64 kDa 
• Atom Count: 5071 
• Modelled Residue Count: 619 
• Deposited Residue Count: 686 
• Unique protein chains: 1

1P7C

Crystal Structure of HSV1-TK complexed with TP5A

• PDB DOI: 10.2210/pdb1P7C/pdb

• Classification: TRANSFERASE
• Organism(s): Human alphaherpesvirus 1 strain 17
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

---

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 

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A, B	343	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: TK OR UL23, TK, UL23 EC: 2.7.1.21
UniProt
Find proteins for P0DTH5 (Human herpesvirus 1 (strain 17)) Explore P0DTH5  Go to UniProtKB:  P0DTH5

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
THM	BindingDB:  1P7C	IC50: 1000 (nM) from 1 assay(s)
		-TΔS: min: 27.18, max: 50.09 (kJ/mol) from 4 assay(s)
		ΔH: min: -7.99e+1, max: -5.71e+1 (kJ/mol) from 4 assay(s)
		ΔG: min: -3.02e+1, max: -2.94e+1 (kJ/mol) from 3 assay(s)

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 = 113.219	α = 90
b = 117.847	β = 90
c = 108.4	γ = 90

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance