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Crystal Structure of HLA-DR1 with CLIP106-120, flipped peptide orientation
Biology and Chemistry Report
3PGC
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM
    Text MHC class II, MHC II, immune system, self antigen, invariant chain, CLIP

    Polymeric Molecules

    Chain A,D
    Description HLA class II histocompatibility antigen, DR alpha chain 
    Fragment UNP residues 26-217 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 22353.4 
    Source Method genetically manipulated  
    Entity Name MHC class II antigen DRA 
    Chain B,E
    Description HLA class II histocompatibility antigen, DRB1-1 beta chain 
    Fragment UNP residues 30-227 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23088.0 
    Source Method genetically manipulated  
    Entity Name MHC class II antigen DRB1*1, DR-1, DR1 
    Chain C,F
    Description HLA class II histocompatibility antigen gamma chain 
    Fragment UNP residues 106-120 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 1734.3 
    Source Method synthetic  
    Entity Name HLA-DR antigens-associated invariant chain, Ia antigen-associated invariant chain, Ii, p33 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    PEG  DI(HYDROXYETHYL)ETHER  C4 H10 O3   106.12  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,D DRA_HUMAN A2BET4     
    B,E 2B11_HUMAN A4F5N0     
    C,F HG2A_HUMAN A8K7R1     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 105266    
     
  •   Gene Details   Hide

    Genetic Source

    Chain B,E
    Common Name Human
    Scientific Name Homo sapiens  
    Gene hla-drb1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET24d


    Chain A,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene hla-dra, hla-dra1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET11a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    5 5q32 972     CD74 molecule, major histocompatibility complex, class II invariant chain CD74    
    6 6p21.3 3122     major histocompatibility complex, class II, DR alpha HLA-DRA    
    6 6p21.3 3123     major histocompatibility complex, class II, DR beta 1 HLA-DRB1    

    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
    rs201781094 LS-SNP   dbSNP   A 76 R - > S Helix 30% (Intermediate) 6_ssto_hap7 3757105
    rs144120198 LS-SNP   dbSNP   A 88 E - > K Beta Ladder 55% (Exposed) 6_ssto_hap7 3757632
    rs138462914 LS-SNP   dbSNP   A 123 R - > Q Beta Ladder 35% (Intermediate) 6_ssto_hap7 3757738
    rs146370028 LS-SNP   dbSNP   A 153 F - > L Beta Ladder 8% (Buried) 6 32411165
    rs200798853 LS-SNP   dbSNP   A 160 V - > I Coil 25% (Intermediate) 6_ssto_hap7 3757848
    rs199723815 LS-SNP   dbSNP   A 168 W - > R Turn 33% (Intermediate) 6_ssto_hap7 3757872
    rs145259888 LS-SNP   dbSNP   C 108 R - > H Coil 69% (Exposed) 5 149786499
    rs139139083 LS-SNP   dbSNP   C 109 M - > T Coil 15% (Intermediate) 5 149786496