hPPARgamma Ligand binding domain in complex with 6-oxoOTE
2VV4
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Receptor
    Structure Weight: 63534.47
    Molecule: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Polymer: 1 Type: protein Length: 276
    Chains: A
    Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475
    Details: 6-OXOOTE
    Organism: Homo sapiens
    Gene Names: Gene View for PPARG NR1C3
    UniProtKB: Protein Feature View | Search PDB | P37231  
    Molecule: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA
    Polymer: 2 Type: protein Length: 276
    Chains: B
    Fragment: LIGAND BINDING DOMAIN, RESIDUES 202-475
    Details: 6-OXOOTE
    Organism: Homo sapiens
    Gene Names: Gene View for PPARG NR1C3
    UniProtKB: Protein Feature View | Search PDB | P37231  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    1FM6   THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THEHETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGANDBINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACIDAND ROSIGLITAZONE AND CO-ACTIVATOR PEPTIDES. 
    1FM9   THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THEHETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGANDBINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACIDAND GI262570 AND CO-ACTIVATOR PEPTIDES. 
    1I7I   CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF HUMANPPAR-GAMMA IN COMPLEX WITH THE AGONIST AZ 242 
    1K74   THE 2.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THEHETERODIMER OF THE HUMAN PPARGAMMA AND RXRALPHA LIGANDBINDING DOMAINS RESPECTIVELY BOUND WITH GW409544 AND 9- CISRETINOIC ACID AND CO-ACTIVATOR PEPTIDES. 
    1KNU   LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATORACTIVATED RECEPTOR GAMMA IN COMPLEX WITH A SYNTHETICAGONIST 
    1NYX   LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATORACTIVATED RECEPTOR GAMMA IN COMPLEX WITH AN AGONIST 
    1PRG   LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA 
    1RDT   CRYSTAL STRUCTURE OF A NEW REXINOID BOUND TO THE RXRALPHALIGAND BINDING DOAMIN IN THE RXRALPHA/PPARGAMMA HETERODIMER 
    1WM0   PPARGAMMA IN COMPLEX WITH A 2-BABA COMPOUND 
    1ZGY   STRUCTURAL AND BIOCHEMICAL BASIS FOR SELECTIVE REPRESSIONOF THE ORPHAN NUCLEAR RECEPTOR LRH -1 BY SHP 
    2F4B   CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF HUMANPPAR-GAMMA IN COMPLEX WITH AN AGONIST 
    2FVJ   A NOVEL ANTI-ADIPOGENIC PARTIAL AGONIST OF PEROXISOMEPROLIFERATOR-ACTIVATED RECEPTOR-GAMMA ( PPARG) RECRUITSPPARG-COACTIVATOR-1 ALPHA ( PGC1A) BUT POTENTIATES INSULINSIGNALING IN VITRO 
    2G0G   STRUCTURE-BASED DRUG DESIGN OF A NOVEL FAMILY OF PPARPARTIAL AGONISTS: VIRTUAL SCREENING, X-RAY CRYSTALLOGRAPHYAND IN VITRO/ IN VIVO BIOLOGICAL ACTIVITIES 
    2G0H   STRUCTURE-BASED DRUG DESIGN OF A NOVEL FAMILY OF PPARPARTIAL AGONISTS: VIRTUAL SCREENING, X-RAY CRYSTALLOGRAPHYAND IN VITRO/ IN VIVO BIOLOGICAL ACTIVITIES 
    2PRG   LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA 
    2VSR   HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH 9-(S)-HODE 
    2VST   HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH 13-(S)-HODE 
    2VV0   HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH DHA 
    2VV1   HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH 4-HDHA 
    2VV2   HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH 5-HEPA 
    2VV3   HPPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH 4-OXODHA 
    3PRG   LIGAND BINDING DOMAIN OF HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR 
    4PRG   0072 PARTIAL AGONIST PPAR GAMMA COCRYSTAL 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    6OB
    Search 
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    6OB C18 H30 O4
    (8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12- dienoic acid
    6OB:2VV4
    6OC
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    6OC C18 H30 O4
    (8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12- dienoic acid
    6OC:2VV4
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly 1       
Biological assembly 1 assigned by authors and generated by PQS (software)
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Itoh, T.,  Fairall, L.,  Schwabe, J.W.R.

    Deposition:   2008-06-02
    Release:   2008-08-19
    Last Modified (REVDAT):   2012-06-06
     
  •   Revision History    Hide
    Mouse over text for details
    2012-06-06
    Non-polymer description
    2012-06-06
    Other
    2012-06-06
    Version format compliance
    2012-06-06
    Refinement description
    2012-06-06
    Source and taxonomy
    2012-06-06
    Biological assembly
    2012-06-06
    Geometry validation
    2012-06-06
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.35
    R-Value: 0.226 (obs.)
    R-Free: 0.252
    Space Group: C 1 2 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 93.78 α = 90.00 
    b = 61.58 β = 103.64 
    c = 118.77 γ = 90.00