An Information Portal to 111558 Biological Macromolecular Structures

PPARgamma in complex with a 2-BABA compound
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text three-layer helical domain, TRANSCRIPTION-SIGNALING PROTEIN COMPLEX

    Polymeric Molecules

    Chain X
    Description Peroxisome proliferator activated receptor gamma 
    Fragment residues 186-477 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 33227.6 
    Source Method genetically manipulated  
    Entity Name PPAR-gamma 
    Chain Y
    Description 14-mer from Nuclear receptor coactivator 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1751.1 
    Source Method synthetic  
    Entity Name NCoA-2, Transcriptional intermediary factor 2, Glucocorticoid receptor-interacting protein 1, GRIP-1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    PLB  2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID  C18 H11 Cl2 N3 O4   404.20  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    X PPARG_HUMAN P37231     
    Y NCOA2_MOUSE Q61026     

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain X
    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   Transcription Factor Activity Sequence Specific DNA Binding  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   RNA Polymerase Ii Transcription Factor Activity Ligand Activated Sequence Specific DNA Binding  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. 

  •   Gene Details   Hide

    Genetic Source

    Chain X
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli bl21(de3)  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET28

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1 A3-A5|1 4.12 cM 17978     nuclear receptor coactivator 2 NCOA2    

    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   X 212 R - > Q Helix 35% (Intermediate) 3 12447480
    rs76480583 LS-SNP   dbSNP   X 238 T - > K Turn 68% (Exposed) 3 12447558
    rs200116144 LS-SNP   dbSNP   X 246 P - > L Coil 19% (Intermediate) 3 12458204
    rs147996578 LS-SNP   dbSNP   X 248 V - > I Beta Ladder 47% (Exposed) 3 12458209
    rs111400984 LS-SNP   dbSNP   X 281 I - > T Helix 13% (Intermediate) 3 12458309 PLB
    rs121909242 LS-SNP   dbSNP   X 286 Q - > P Helix 7% (Buried) 3 12458324
    rs28936407 LS-SNP   dbSNP   X 288 R - > H Helix 29% (Intermediate) 3 12458330 PLB
    rs72551362 LS-SNP   dbSNP   X 290 V - > M Helix 11% (Intermediate) 3 12458335
    rs139894525 LS-SNP   dbSNP   X 307 V - > L 3/10 Helix 58% (Exposed) 3 12458386
    rs145566594 LS-SNP   dbSNP   X 328 T - > P Helix 1% (Buried) 3 12458449
    rs141683496 LS-SNP   dbSNP   X 343 E - > K Turn 33% (Intermediate) 3 12458494 PLB
    rs140204299 LS-SNP   dbSNP   X 357 R - > Q Coil 32% (Intermediate) 3 12458537
    rs188622140 LS-SNP   dbSNP   X 360 F - > C 3/10 Helix 2% (Buried) 3 12458546
    rs72551363 LS-SNP   dbSNP   X 360 F - > L 3/10 Helix 2% (Buried) 3 12458547
    rs148844673 LS-SNP   dbSNP   X 382 S - > R Helix 29% (Intermediate) 3 12458613
    rs72551364 LS-SNP   dbSNP   X 397 R - > C Coil 4% (Buried) 3 12475399
    rs186728157 LS-SNP   dbSNP   X 427 E - > A Turn 95% (Exposed) 3 12475490
    rs62243567 LS-SNP   dbSNP   X 449 H - > N Helix 13% (Intermediate) 3 12475555
    rs201781800 LS-SNP   dbSNP   X 459 T - > M Turn 56% (Exposed) 3 12475586
    rs121909244 LS-SNP   dbSNP   X 467 P - > L Helix 54% (Exposed) 3 12475610