4JBX | pdb_00004jbx

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with SK-78

• PDB DOI: https://doi.org/10.2210/pdb4JBX/pdb

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


• Deposited: 2013-02-20 Released: 2013-03-06 
• Deposition Author(s): Pernot, L., Novakovic, I., Westermaier, Y., Perozzo, R., Raic-Malic, S., Scapozza, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer

Pernot, L., Novakovic, I., Perozzo, R., Raic-Malic, S., Scapozza, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 72.91 kDa 
• Atom Count: 5,066 
• Modeled Residue Count: 619 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A, B	332	Human alphaherpesvirus 1 strain 17	Mutation(s): 0  Gene Names: TK, TK (UL23), 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
SK7	C [auth A], G [auth B]	6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione C10 H14 N2 O4 BIORUVJYBNBNNA-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.486	α = 90
b = 118.314	β = 90
c = 108.234	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Pernot, L., Novakovic, I., Westermaier, Y., Perozzo, R., Raic-Malic, S., Scapozza, L.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Experimental preparation, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description