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Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text zinc finger, transcription, histone, lysine methyaltion, nuclear protein, TRANSFERASE-NUCLEAR PROTEIN complex

    Polymeric Molecules

    Chain A,D
    Description Histone-lysine N-methyltransferase NSD3 
    Fragment UNP RESIDUES 1310-1413 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 12058.8 
    Source Method genetically manipulated  
    Entity Name Nuclear SET domain-containing protein 3, Protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1, WHSC1-like protein 1 
    Chain B,F
    Description Histone H3.3 
    Fragment UNP RESIDUES 2-16 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 1607.9 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    ZN  ZINC ION  Zn   65.41  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,D NSD3_HUMAN Q9BZ95     
    B,F H33_HUMAN P84243     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A D      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,D
    GO ID   Ontology GO Term Definition
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 

  •   Gene Details   Hide

    Genetic Source

    Chain A,D
    Scientific Name Homo sapiens  
    Gene whsc1l1, nsd3, dc28
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q42.12 3020     H3 histone, family 3A H3F3A    
    8 8p11.2 54904     Wolf-Hirschhorn syndrome candidate 1-like 1 WHSC1L1    
    17 17q25.1 3021     H3 histone, family 3B (H3.3B) H3F3B    

    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
    rs201199873 LS-SNP   dbSNP   A 1366 Q - > R Beta 50% (Exposed) 8 38133376