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Revealing a marine natural product as a novel agonist for retinoic acid receptors with a unique binding mode and antitumor activity
Biology and Chemistry Report
4DQM
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION/TRANSFERASE
    Text nuclear receptor transcription factor, ligand binding domain, Transcription regulation, Nucleus, TRANSCRIPTION-TRANSFERASE complex

    Polymeric Molecules

    Chain A,C
    Description Retinoic acid receptor alpha 
    Fragment ligand binding domain, UNP RESIDUES 182-415 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 26486.1 
    Source Method genetically manipulated  
    Entity Name RAR-alpha, Nuclear receptor subfamily 1 group B member 1 
    Chain B,D
    Description Nuclear receptor coactivator 1 
    Fragment LXXLL motif 7, UNP RESIDUES 1432-1441 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1173.4 
    Source Method synthetic  
    Entity Name NCoA-1, Class E basic helix-loop-helix protein 74, bHLHe74, Protein Hin-2, RIP160, Renal carcinoma antigen NY-REN-52, Steroid receptor coactivator 1, SRC-1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    LUF  (5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethylcyclohex-1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxyfuran-2(5H)-one  C25 H38 O3   386.57  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C RARA_HUMAN B8Y636     
    B,D NCOA1_HUMAN O00150     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    B D  2.3.1.48      
     
  •   Gene Details   Hide

    Genetic Source

    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Gene nr1b1, rara
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET24a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    2 2p23 8648     nuclear receptor coactivator 1 NCOA1    
    17 17q21 5914     retinoic acid receptor, alpha RARA    

    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
    rs79997555 LS-SNP   dbSNP   A 186 E - > G Helix 54% (Exposed) 17 38508249
    rs79997555 LS-SNP   dbSNP   A 186 E - > G Helix 54% (Exposed) 17 38508249
    rs112626578 LS-SNP   dbSNP   A 187 L - > P Helix 13% (Intermediate) 17 38508252
    rs112626578 LS-SNP   dbSNP   A 187 L - > P Helix 13% (Intermediate) 17 38508252
    rs201919660 LS-SNP   dbSNP   A 225 W - > R Helix 10% (Intermediate) 17 38508625 NULL
    rs201919660 LS-SNP   dbSNP   A 225 W - > R Helix 10% (Intermediate) 17 38508625 NULL
    rs200827868 LS-SNP   dbSNP   A 248 G - > D Turn 27% (Intermediate) 17 38508695
    rs200827868 LS-SNP   dbSNP   A 248 G - > D Turn 27% (Intermediate) 17 38508695
    rs145829003 LS-SNP   dbSNP   A 318 P - > R 3/10 Helix 71% (Exposed) 17 38510699
    rs145829003 LS-SNP   dbSNP   A 318 P - > R 3/10 Helix 71% (Exposed) 17 38510699
    rs148999974 LS-SNP   dbSNP   A 323 D - > E Helix 23% (Intermediate) 17 38510715
    rs148999974 LS-SNP   dbSNP   A 323 D - > E Helix 23% (Intermediate) 17 38510715