1D8E

Zinc-depleted FTase complexed with K-RAS4B peptide substrate and FPP analog.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FARNESYLTRANSFERASE (ALPHA SUBUNIT)377Rattus norvegicusMutation(s): 0 
EC: 2.5.1.21
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
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UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FARNESYLTRANSFERASE (BETA SUBUNIT)437Rattus norvegicusMutation(s): 0 
EC: 2.5.1.21
UniProt
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
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UniProt GroupQ02293
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence 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
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FII
Query on FII

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

Download Ideal Coordinates CCD File 
D [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.411α = 90
b = 171.411β = 90
c = 69.663γ = 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: 2000-03-20
    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: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-03-13
    Changes: Source and taxonomy, Structure summary