Macromolecule Content

Total Structure Weight: 72.93 kDa
Atom Count: 5056
Residue Count: 619
Unique protein chains: 1

4OQM

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

DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.220
R-Value Work: 0.168
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

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.

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDU Query on FDU Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain H [B] MOL2 format, chain C [A] MOL2 format, chain H [B]	A, B	1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-ethynylpyrimidine-2,4(1H,3H)-dione C₁₁ H₁₁ F N₂ O₅ YEEGMPUOCRQFRV-IBCQBUCCSA-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 F [A] SDF format, chain G [A] SDF format, chain I [B] SDF format, chain J [B] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain I [B] MOL2 format, chain J [B]	A, B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.220
R-Value Work: 0.168
R-Value Observed: 0.171
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-02-10
Released Date: 2014-08-13

Deposition Author(s):

Westermaier, Y.

Revision History

Version 1.0: 2014-08-13
Type: Initial release

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.