2AWH

Human Nuclear Receptor-Ligand Complex 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Recombinant Human PPAR-beta/delta Ligand-binding Domain is Locked in an Activated Conformation by Endogenous Fatty Acids

Fyffe, S.A.Alphey, M.S.Buetow, L.Smith, T.K.Ferguson, M.A.J.Sorensen, M.D.Bjorkling, F.Hunter, W.N.

(2006) J Mol Biol 356: 1005-1013

  • DOI: 10.1016/j.jmb.2005.12.047
  • Primary Citation of Related Structures:  
    2B50, 2AWH

  • PubMed Abstract: 
  • High-resolution crystallographic structures of recombinant human peroxisome proliferator-activated receptor ligand-binding domain (isotype beta/delta) reveal a fatty acid in the binding site. Mass spectrometry confirmed the presence of C16:0, C16:1, ...

    High-resolution crystallographic structures of recombinant human peroxisome proliferator-activated receptor ligand-binding domain (isotype beta/delta) reveal a fatty acid in the binding site. Mass spectrometry confirmed the presence of C16:0, C16:1, C18:0 and C18:1 in a ratio of approximately 3:2:1:4 with 11, Z-octadecenoic acid (cis-vaccenic acid) identified as the predominant species. These are endogenous fatty acids acquired from the bacterial expression system, and serve to lock the ligand-binding domain into the activated conformation. A requirement for crystal growth, the additive n-heptyl-beta-d-glucopyranoside, binds near the activation function helix where recognition of co-activator proteins occurs. Our observations suggest potential physiological ligands for human PPAR-beta/delta and highlight that reported binding studies must be treated with caution unless endogenous fatty acids have been removed from the sample prior to analysis.


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxisome proliferator activated receptor deltaAB268Homo sapiensMutation(s): 0 
Gene Names: PPARDNR1C2PPARB
Find proteins for Q03181 (Homo sapiens)
Explore Q03181 
Go to UniProtKB:  Q03181
NIH Common Fund Data Resources
PHAROS  Q03181
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VCA
Query on VCA

Download CCD File 
A, B
VACCENIC ACID
C18 H34 O2
UWHZIFQPPBDJPM-FPLPWBNLSA-N
 Ligand Interaction
B7G
Query on B7G

Download CCD File 
A, B
heptyl beta-D-glucopyranoside
C13 H26 O6
NIDYWHLDTIVRJT-UJPOAAIJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.22α = 90
b = 96.717β = 89.96
c = 92.304γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary