6Y08

Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole

• PDB DOI: https://doi.org/10.2210/pdb6Y08/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-06 Released: 2021-02-17 
• Deposition Author(s): Maj, P., Jarmula, A., Wilk, P., Weiss, M.S., Rode, W.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole

Maj, P., Jarmula, A., Wilk, P., Weiss, M.S., Rode, W.

To be published.

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: 71.12 kDa 
• Atom Count: 4,630 
• Modelled Residue Count: 557 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	307	Mus musculus	Mutation(s): 0  Gene Names: Tyms EC: 2.1.1.45
UniProt
Find proteins for P07607 (Mus musculus) Explore P07607  Go to UniProtKB:  P07607

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
08D (Subject of Investigation/LOI)	D [auth A], F [auth B]	Sulfamethoxazole C10 H11 N3 O3 S JLKIGFTWXXRPMT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.545	α = 90
b = 88.057	β = 96.15
c = 68.262	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Maj, P., Jarmula, A., Wilk, P., Weiss, M.S., Rode, W.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2016/21/B/NZ1/00288

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description