28JN | pdb_000028jn

CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A-176120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.251 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

KRAS Can Bind to FTase Despite Disruption of the CAAX Binding Site.

Carion, M.Cuesta, R.Kowalczyk, D.Smets, W.Soons, E.Klaassen, H.Vanderhoydonck, B.Marchand, A.Versele, M.Chaltin, P.Dedecker, P.Park, H.Ismail, S.

(2026) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.5c00732
  • Primary Citation of Related Structures:  
    28JN

  • PubMed Abstract: 

    Protein prenylation is a post-translational modification promoting membrane association where isoprenoid lipids attach to C-terminal cysteines of eukaryotic proteins such as Ras and Rho GTPases, nucleus lamins, and G-protein subunits. Three enzymes catalyze this process: farnesyltransferase (FTase) and geranylgeranyltransferase type I and II (GGTase I and RabGGTase). FTase and GGTase-I recognize C-terminal CaaX motifs, of which the terminal amino acid confers specificity. Due to its involvement in oncogenic Ras activation, FTase has become a major anticancer target for drug development. Although first-generation FTase inhibitors failed in clinical trials in many cancers due to compensatory geranylgeranylation of KRAS and NRAS, they remain effective against HRAS-driven tumors and other pathologies, such as Hutchinson-Gilford progeria syndrome. The FTase inhibitor A-176120 was reported to compete with farnesyl and not KRAS. However, our crystallographic and biochemical analyses reveal that A-176120 sterically interferes with the engagement of the KRAS CAAX motif, reducing, but not abolishing, its binding to FTase.


  • Organizational Affiliation
    • Department of Chemistry, Biochemistry, Molecular and Structural Biology Division, KU Leuven, 3001 Heverlee, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase subunit beta437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
UniProt
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02293
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.251 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.777α = 90
b = 172.777β = 90
c = 70.489γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KU LeuvenBelgium3E210862

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-04
    Type: Initial release