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LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA IN COMPLEX WITH A SYNTHETIC AGONIST
Biology and Chemistry Report
1KNU
  •   Structure Details   Hide

    Structure Keywords

    Keywords DNA BINDING PROTEIN
    Text PPAR, NUCLEAR RECEPTOR, TRANSCRIPTION, GENE REGULATION, AGONIST COMPLEX, DNA BINDING PROTEIN

    Polymeric Molecules

    Chain A,B
    Description PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA 
    Fragment LIGAND BINDING DOMAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 31321.7 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    YPA  (S)-3-(4-(2-CARBAZOL-9-YL-ETHOXY)-PHENYL)-2-ETHOXY-PROPIONIC ACID  C25 H25 N O4   403.47  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B PPARG_HUMAN A8K3G6     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    43401   Steroid Hormone Mediated Signaling Pathway  A Series of Molecular Signals Mediated by a Steroid Hormone Binding to a Receptor. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3700   Sequence Specific DNA Binding Transcription Factor Activity  Interacting Selectively and Non Covalently with a Specific DNA Sequence in Order to Modulate Transcription. the Transcription Factor May or May Not Also Interact Selectively with a Protein or Macromolecular Complex. 
    3707   Steroid Hormone Receptor Activity  Combining with a Steroid Hormone and Transmitting the Signal Within the Cell to Initiate a Change in Cell Activity or Function. 
    4879   Ligand Activated Sequence Specific DNA Binding RNA Polymerase Ii Transcription Factor Activity  Combining with a Signal and Transmitting the Signal to the Transcriptional Machinery by Interacting Selectively and Non Covalently with a Specific DNA Sequence in Order to Modulate Transcription by RNA Polymerase Ii. 


    Protein Analyses

    Measured Binding Affinities   

     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Tissue Adipose Tissue
    Gene pparg, nr1c3
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21de3
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-3X-hPPARgLBD


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p25 5468     peroxisome proliferator-activated receptor gamma PPARG    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs150296212 LS-SNP   dbSNP   A 212 R - > Q Helix 22% (Intermediate) 3 12447480
    rs76480583 LS-SNP   dbSNP   A 238 T - > K Turn 58% (Exposed) 3 12447558
    rs200116144 LS-SNP   dbSNP   A 246 P - > L Coil 24% (Intermediate) 3 12458204
    rs147996578 LS-SNP   dbSNP   A 248 V - > I Beta Ladder 42% (Exposed) 3 12458209
    rs111400984 LS-SNP   dbSNP   A 281 I - > T Helix 14% (Intermediate) 3 12458309 YPA
    rs121909242 LS-SNP   dbSNP   A 286 Q - > P Helix 7% (Buried) 3 12458324 YPA
    rs28936407 LS-SNP   dbSNP   A 288 R - > H Helix 43% (Exposed) 3 12458330 YPA
    rs72551362 LS-SNP   dbSNP   A 290 V - > M Helix 4% (Buried) 3 12458335
    rs139894525 LS-SNP   dbSNP   A 307 V - > L 3/10 Helix 51% (Exposed) 3 12458386
    rs145566594 LS-SNP   dbSNP   A 328 T - > P Helix 0% (Buried) 3 12458449
    rs141683496 LS-SNP   dbSNP   A 343 E - > K 3/10 Helix 65% (Exposed) 3 12458494 YPA
    rs140204299 LS-SNP   dbSNP   A 357 R - > Q Bend 31% (Intermediate) 3 12458537
    rs188622140 LS-SNP   dbSNP   A 360 F - > C 3/10 Helix 4% (Buried) 3 12458546
    rs72551363 LS-SNP   dbSNP   A 360 F - > L 3/10 Helix 4% (Buried) 3 12458547
    rs148844673 LS-SNP   dbSNP   A 382 S - > R Helix 15% (Intermediate) 3 12458613
    rs72551364 LS-SNP   dbSNP   A 397 R - > C Bend 5% (Buried) 3 12475399
    rs186728157 LS-SNP   dbSNP   A 427 E - > A Turn 73% (Exposed) 3 12475490
    rs62243567 LS-SNP   dbSNP   A 449 H - > N Helix 16% (Intermediate) 3 12475555 YPA
    rs201781800 LS-SNP   dbSNP   A 459 T - > M Helix 56% (Exposed) 3 12475586
    rs121909244 LS-SNP   dbSNP   A 467 P - > L Helix 64% (Exposed) 3 12475610