4OQM | pdb_00004oqm

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU

• PDB DOI: https://doi.org/10.2210/pdb4OQM/pdb

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


• Deposited: 2014-02-10 Released: 2014-08-13 
• Deposition Author(s): Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with F-ARA-EdU

Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., 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: 72.93 kDa 
• Atom Count: 5,056 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDU	C [auth A], H [auth B]	1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione C11 H11 F N2 O5 YEEGMPUOCRQFRV-IBCQBUCCSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.44	α = 90
b = 115.31	β = 90
c = 107.9	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: 2014-08-13 
Deposition Author(s): Pernot, L., Neef, A.B., Westermaier, Y., Perozzo, R., Luedtke, N., Scapozza, L.

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description