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 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.febslet.2007.05.080
  • Structures With Same Primary Citation

  • 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 (r ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carnitine O-palmitoyltransferase 2A, B653Rattus norvegicusMutation(s): 0 
Gene Names: Cpt2Cpt-2
EC: 2.3.1.21
Find proteins for P18886 (Rattus norvegicus)
Explore P18886 
Go to UniProtKB:  P18886
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BUJ
Query on BUJ

Download CCD File 
A, B
(3R)-3-(hexadecanoylamino)-4-(trimethylammonio)butanoate
C23 H46 N2 O3
IUBZDMWVMKIBIS-OAQYLSRUSA-N
 Ligand Interaction
BOG
Query on BOG

Download CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BUJIC50:  210   nM  Binding MOAD
BUJIC50 :  210   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • 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

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Entry History 

Deposition Data

Revision History 

  • 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