4FGT

Allosteric peptidic inhibitor of human thymidylate synthase that stabilizes inactive conformation of the enzyme.

• PDB DOI: https://doi.org/10.2210/pdb4FGT/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-06-04 Released: 2013-03-06 
• Deposition Author(s): Tochowicz, A., Finer-Moore, J., Stroud, R.M., Costi, M.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.229 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Alanine mutants of the interface residues of human thymidylate synthase decode key features of the binding mode of allosteric anticancer peptides.

Tochowicz, A., Santucci, M., Saxena, P., Guaitoli, G., Trande, M., Finer-Moore, J., Stroud, R.M., Costi, M.P.

(2015) J Med Chem 58: 1012-1018

• PubMed: 25427005 
• DOI: https://doi.org/10.1021/jm5011176
• Primary Citation of Related Structures:  
  4FGT


• PubMed Abstract: 
  

  Allosteric peptide inhibitors of thymidylate synthase (hTS) bind to the dimer interface and stabilize the inactive form of the protein. Four interface residues were mutated to alanine, and interaction studies were employed to decode the key role of these residues in the peptide molecular recognition. This led to the identification of three crucial interface residues F59, L198, and Y202 that impart activity to the peptide inhibitors and suggest the binding area for further inhibitor design.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of California-San Francisco , 600 16th Street, San Francisco, California 94158, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 38.08 kDa 
• Atom Count: 2,326 
• Modelled Residue Count: 271 
• Deposited Residue Count: 329 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	325	Homo sapiens	Mutation(s): 1  Gene Names: TYMS, TS, OK/SW-cl.29 EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens) Explore P04818  Go to UniProtKB:  P04818
PHAROS:  P04818 GTEx:  ENSG00000176890

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CG peptide	B [auth D]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.229 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.807	α = 90
b = 95.807	β = 90
c = 83.285	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Tochowicz, A., Finer-Moore, J., Stroud, R.M., Costi, M.P.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary