Macromolecule Content

Total Structure Weight: 72.82 kDa
Atom Count: 5155
Residue Count: 625
Unique protein chains: 1

4JBY

Crystal structure of thymidine kinase from Herpes simplex virus type 1 in complex with F-SK78

DOI: 10.2210/pdb4JBY/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

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
Find proteins for P03176 (Human herpesvirus 1 (strain 17)) Explore P03176 Go to UniProtKB: P03176
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSK Query on FSK Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain F [B] MOL2 format, chain C [A] MOL2 format, chain F [B]	A, B	6-[(1Z)-3-fluoro-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione C₁₀ H₁₃ F N₂ O₃ NEZZLCCSEJKABY-XVNBXDOJSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] SDF format, chain G [B] SDF format, chain H [B] SDF format, chain I [B] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain G [B] MOL2 format, chain H [B] MOL2 format, chain I [B]	A, B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [B] MOL2 format, chain J [B]	B	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.218
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.166	α = 90
b = 116.569	β = 90
c = 108.309	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2013-02-20
Released Date: 2013-03-06

Deposition Author(s):

Westermaier, Y.

Revision History

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2013-10-02
Changes: Experimental preparation, Structure summary

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.