2TMK | pdb_00002tmk

YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)

• PDB DOI: https://doi.org/10.2210/pdb2TMK/pdb

• Classification: PHOSPHOTRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-06-12 Released: 1998-06-17 
• Deposition Author(s): Lavie, A., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.253 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.

Lavie, A., Vetter, I.R., Konrad, M., Goody, R.S., Reinstein, J., Schlichting, I.

(1997) Nat Struct Biol 4: 601-604

• PubMed: 9253404 
• DOI: https://doi.org/10.1038/nsb0897-601
• Primary Citation Related Structures: 
  1TMK, 2TMK

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: 50.33 kDa 
• Atom Count: 3,518 
• Modeled Residue Count: 408 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE KINASE	A, B	216	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CDC8 EC: 2.7.4.9
UniProt
Find proteins for P00572 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00572  Go to UniProtKB:  P00572

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATM	D [auth A], F [auth B]	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P OIFWQOKDSPDILA-XLPZGREQSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.253 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.42	α = 90
b = 144.2	β = 110.9
c = 49.72	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Lavie, A., Schlichting, I.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection, Other
• Version 1.4: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection