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: https://doi.org/10.1021/bi981197z
  • Primary Citation of Related Structures:  
    1QBQ

  • 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, 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FPT ALPHA-SUBUNIT333Rattus norvegicusMutation(s): 0 
EC: 2.5.1
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FPT BETA-SUBUNIT437Rattus norvegicusMutation(s): 0 
EC: 2.5.1
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

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYL-CYS-VAL-ILE-SELENOMET-COOH PEPTIDEC [auth P]5N/AMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HFP
Query on HFP

Download Ideal Coordinates CCD File 
F [auth B]ALPHA-HYDROXYFARNESYLPHOSPHONIC ACID
C15 H33 O4 P
IJNCEETVCWDDQB-KFWWJZLASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
C [auth P]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
HFP Binding MOAD:  1QBQ Ki: 5 (nM) from 1 assay(s)
PDBBind:  1QBQ Ki: 5 (nM) from 1 assay(s)
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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