1QBQ

STRUCTURE OF RAT FARNESYL PROTEIN TRANSFERASE COMPLEXED WITH A CVIM PEPTIDE AND ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue

Strickland, C.L.Windsor, W.T.Syto, R.Wang, L.Bond, R.Wu, Z.Schwartz, J.Le, H.V.Beese, L.S.Weber, P.C.

(1998) Biochemistry 37: 16601-16611

  • DOI: 10.1021/bi981197z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystallographic structure of acetyl-Cys-Val-Ile-selenoMet-COOH and alpha-hydroxyfarnesylphosphonic acid (alphaHFP) complexed with rat farnesyl protein transferase (FPT) (space group P61, a = b = 174. 13 A, c = 69.71 A, alpha = beta = 90 degrees, ...

    The crystallographic structure of acetyl-Cys-Val-Ile-selenoMet-COOH and alpha-hydroxyfarnesylphosphonic acid (alphaHFP) complexed with rat farnesyl protein transferase (FPT) (space group P61, a = b = 174. 13 A, c = 69.71 A, alpha = beta = 90 degrees, gamma = 120 degrees, Rfactor = 21.8%, Rfree = 29.2%, 2.5 A resolution) is reported. In the ternary complex, the bound substrates are within van der Waals contact of each other and the FPT enzyme. alphaHFP binds in an extended conformation in the active-site cavity where positively charged side chains and solvent molecules interact with the phosphate moiety and aromatic side chains pack adjacent to the isoprenoid chain. The backbone of the bound CaaX peptide adopts an extended conformation, and the side chains interact with both FPT and alphaHFP. The cysteine sulfur of the bound peptide coordinates the active-site zinc. Overall, peptide binding and recognition appear to be dominated by side-chain interactions. Comparison of the structures of the ternary complex and unliganded FPT [Park, H., Boduluri, S., Moomaw, J., Casey, P., and Beese, L. (1997) Science 275, 1800-1804] shows that major rearrangements of several active site side chains occur upon substrate binding.


    Related Citations: 
    • Engineering of protein farnesyl transferase for co-crystallization. Expression, purification and kinetic characterization of Beta-subunit C-terminal mutants.
      Wu, Z., Demma, M., Strickland, C.L., Syto, R., Le, H.V., Weber, P.C., Windsor, W.T.
      (1999) Protein Eng 12: 101

    Organizational Affiliation

    Structural Chemistry Department, Schering-Plough Research Institute, Kenilworth, New Jersey 07033-0539, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FPT ALPHA-SUBUNIT
A
333Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
Find proteins for Q04631 (Rattus norvegicus)
Go to UniProtKB:  Q04631

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FPT BETA-SUBUNIT
B
437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1 (PDB Primary Data), 2.5.1.58 (UniProt)
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ACETYL-CYS-VAL-ILE-SELENOMET-COOH PEPTIDE
P
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HFP
Query on HFP

Download CCD File 
B
ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID
C15 H33 O4 P
IJNCEETVCWDDQB-KFWWJZLASA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HFPKi:  5   nM  Binding MOAD
HFPKi:  5   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.218 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.132α = 90
b = 174.132β = 90
c = 69.705γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description