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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.213 (DCC)
R-Value Work:
0.174 (Depositor), 0.176 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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.

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

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| 3D 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
UniProt
Find proteins for P0DTH5 (Human herpesvirus 1 (strain 17)) Explore P0DTH5 Go to UniProtKB: P0DTH5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SK7 Query on SK7 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	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		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.213 (DCC)
R-Value Work: 0.174 (Depositor), 0.176 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Revision History (Full details and data files)

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

4JBX | pdb_00004jbx

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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