6GKO | pdb_00006gko

Mouse thymidylate synthase cocrystallized with dUMP and soaked in phenolphthalein

• PDB DOI: https://doi.org/10.2210/pdb6GKO/pdb

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


• Deposited: 2018-05-21 Released: 2019-06-05 
• Deposition Author(s): Maj, P., Wilk, P., Jarmula, A., Weiss, M.S., Rode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Thymidylate synthase fragment screening

Maj, P., Wilk, P., Jarmula, A., 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: 71.41 kDa 
• Atom Count: 5,081 
• Modeled Residue Count: 571 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FGT	D [auth A], G [auth B]	3,3-bis(4-hydroxyphenyl)-2-benzofuran-1-one C20 H14 O4 KJFMBFZCATUALV-UHFFFAOYSA-N
UMP	C [auth A], F [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
DMS	E [auth A], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FGT	BindingDB:  6GKO	Ki: 1200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.701	α = 90
b = 87.441	β = 96.02
c = 68.515	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Maj, P., Wilk, P., Jarmula, A., Weiss, M.S., Rode, W.

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description