8Y7W | pdb_00008y7w

Thymidine Kinase from Staphylococcus aureus(COL strain)

• PDB DOI: https://doi.org/10.2210/pdb8Y7W/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-05 Released: 2025-02-12 
• Deposition Author(s): Ashraf, A., Pal, R.K., Hassan, M.I.
• Funding Organization(s): Indian Council of Medical Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Thymidine Kinase from Staphylococcus aureus(COL strain)

Ashraf, A., Pal, R.K., Hassan, M.I.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.31 kDa 
• Atom Count: 1,428 
• Modeled Residue Count: 179 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A	205	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: tdk, SACOL2111 EC: 2.7.1.21
UniProt
Find proteins for Q5HE81 (Staphylococcus aureus (strain COL)) Explore Q5HE81  Go to UniProtKB:  Q5HE81

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.736	α = 90
b = 71.736	β = 90
c = 95.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Ashraf, A., Pal, R.K., Hassan, M.I.

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Funding Organization	Location	Grant Number
Indian Council of Medical Research	India	No.R.1201/06/2022-HR/E

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release