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Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D
Biology and Chemistry Report
1Z5L
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM
    Text Ig fold, MHC fold, IMMUNE SYSTEM

    Polymeric Molecules

    Chain A,C
    Description T-cell surface glycoprotein CD1d antigen 
    Fragment extracellular domain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 32632.9 
    Source Method genetically manipulated  
    Chain B,D
    Description Beta-2-microglobulin 
    Fragment extracellular domain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11660.4 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
    PBS  (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL  C32 H63 N O9   605.84  View 
    R16  HEXADECANE  C16 H34   226.44  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C CD1D1_MOUSE P11609     
    B,D B2MG_MOUSE P01887     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 159251    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B,D
    GO ID   Ontology GO Term Definition
    2376   Immune System Process  Any Process Involved in the Development or Functioning of the Immune System an Organismal System For Calibrated Responses to Potential Internal or Invasive Threats. 
    2474   Antigen Processing and Presentation of Peptide Antigen Via Mhc Class I  The Process in Which an Antigen Presenting Cell Expresses a Peptide Antigen On Its Cell Surface in Association with an Mhc Class I Protein Complex. Class I Here Refers to Classical Class I Molecules. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    42612   Mhc Class I Protein Complex  A Transmembrane Protein Complex Composed of a Mhc Class I Alpha Chain and an Invariant Beta2 Microglobin Chain and with or Without a Bound Peptide Antigen. Class I Here Refers to Classical Class I Molecules. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B,D
    Common Name House Mouse
    Scientific Name Mus musculus  
    Genus Mus
    Host Common Name Fruit Fly
    Host Scientific Name Drosophila melanogaster  
    Host Genus Drosophila
    Host Cell Type S2 Cells
    Host Vector Type Plasmid
    Host Plasmid Name pRMHa3


    Chain A,C
    Common Name House Mouse
    Scientific Name Mus musculus  
    Genus Mus
    Host Common Name Fruit Fly
    Host Scientific Name Drosophila melanogaster  
    Host Genus Drosophila
    Host Cell Type S2 Cells
    Host Vector Type Plasmid
    Host Plasmid Name pRMHa3