1D8D

CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A K-RAS4B PEPTIDE SUBSTRATE AND FPP ANALOG AT 2.0A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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This is version 1.2 of the entry. See complete history


Literature

The basis for K-Ras4B binding specificity to protein farnesyltransferase revealed by 2 A resolution ternary complex structures.

Long, S.B.Casey, P.J.Beese, L.S.

(2000) Structure 8: 209-222

  • DOI: 10.1016/s0969-2126(00)00096-4
  • Primary Citation of Related Structures:  
    1D8D, 1D8E

  • PubMed Abstract: 
  • The protein farnesyltransferase (FTase) catalyzes addition of the hydrophobic farnesyl isoprenoid to a cysteine residue fourth from the C terminus of several protein acceptors that are essential for cellular signal transduction such as Ras and Rho. This addition is necessary for the biological function of the modified proteins ...

    The protein farnesyltransferase (FTase) catalyzes addition of the hydrophobic farnesyl isoprenoid to a cysteine residue fourth from the C terminus of several protein acceptors that are essential for cellular signal transduction such as Ras and Rho. This addition is necessary for the biological function of the modified proteins. The majority of Ras-related human cancers are associated with oncogenic variants of K-RasB, which is the highest affinity natural substrate of FTase. Inhibition of FTase causes regression of Ras-mediated tumors in animal models.


    Related Citations: 
    • Crystal Structure of Protein Farnesyltransferase at 2.25A Resolution
      Park, H.-W., Boduluri, S.R., Moomaw, J.F., Casey, P.J., Beese, L.S.
      (1997) Science 275: 1800
    • Co-crystal Structure of Mammalian Protein Farnesyltransferase with a Farnesyl Diphosphate Substrate
      Long, S.B., Casey, P.J., Beese, L.S.
      (1998) Biochemistry 37: 9612

    Organizational Affiliation

    Department of Biochemistry, PO Box 3711, Duke University Medical Center, Durham, 27710, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
farnesyltransferase (alpha subunit)A377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.21 (PDB Primary Data), 2.5.1.58 (UniProt), 2.5.1.59 (UniProt)
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
farnesyltransferase (beta subunit)B437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.21 (PDB Primary Data), 2.5.1.58 (UniProt)
UniProt
Find proteins for Q02293 (Rattus norvegicus)
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Go to UniProtKB:  Q02293
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
K-RAS4B PEPTIDE SUBSTRATEC [auth P]11N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FII (Subject of Investigation/LOI)
Query on FII

Download Ideal Coordinates CCD File 
G [auth B][(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID
C17 H30 N O5 P
JAOBYUCYSAOLHS-XGGJEREUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth B], F [auth B], H [auth P], I [auth P]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.919α = 90
b = 170.919β = 90
c = 69.284γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance