4IVR | pdb_00004ivr

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with IN52/10

• PDB DOI: https://doi.org/10.2210/pdb4IVR/pdb

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


• Deposited: 2013-01-23 Released: 2013-02-06 
• 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: 2.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.199 (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: 72.23 kDa 
• Atom Count: 4,893 
• Modeled Residue Count: 616 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A, B	331	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N50	C [auth A], E [auth B]	2-[(2,6-dimethoxy-5-methylpyrimidin-4-yl)methylidene]propane-1,3-diol C11 H16 N2 O4 YLFWDZOXQQHLDL-UHFFFAOYSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.042	α = 90
b = 115.127	β = 90
c = 108.075	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: 2013-02-06 
Deposition Author(s): Pernot, L., Novakovic, I., Westermaier, Y., Perozzo, R., Raic-Malic, S., Scapozza, L.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Experimental preparation, Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description