2RCU

Crystal structure of rat carnitine palmitoyltransferase 2 in complex with r-3-(hexadecanoylamino)-4-(trimethylazaniumyl)butanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BUJClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

Carnitine palmitoyltransferase 2: analysis of membrane association and complex structure with a substrate analog.

Rufer, A.C.Lomize, A.Benz, J.Chomienne, O.Thoma, R.Hennig, M.

(2007) FEBS Lett 581: 3247-3252

  • DOI: https://doi.org/10.1016/j.febslet.2007.05.080
  • Primary Citation of Related Structures:  
    2RCU

  • PubMed Abstract: 

    The mitochondrial membrane-associated carnitine palmitoyltransferase system is a validated target for the treatment of type 2 diabetes mellitus. To further facilitate structure-based drug discovery, we determined the crystal structure of rat CPT-2 (rCPT-2) in complex with the substrate analogue palmitoyl-aminocarnitine at 1.8A resolution. Biochemical analyses revealed a strong effect of this compound on rCPT-2 activity and stability. Using a computational approach we examined the membrane association of rCPT-2. The protein interacts with the membrane as a functional monomer and the calculations confirm the presence of a membrane association domain that consists of layers of hydrophobic and positively charged residues.


  • Organizational Affiliation

    F Hoffmann-La Roche AG, Pharma Research Discovery, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carnitine O-palmitoyltransferase 2
A, B
653Rattus norvegicusMutation(s): 0 
Gene Names: Cpt2Cpt-2
EC: 2.3.1.21
UniProt
Find proteins for P18886 (Rattus norvegicus)
Explore P18886 
Go to UniProtKB:  P18886
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18886
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.273α = 90
b = 97.75β = 90
c = 312.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BUJClick on this verticalbar to view detailsBest fitted BOGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-09-25
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2021-05-05
    Changes: Data collection, Structure summary
  • Version 1.6: 2023-08-30
    Changes: Data collection, Database references, Refinement description