Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2
Primary Citation
  •   Molecular Description Hide
    Classification: Immune System
    Structure Weight: 72849.55
    Molecule: HLA class II histocompatibility antigen, DR alpha chain
    Polymer: 1 Type: protein Length: 183
    Chains: A
    Fragment: Extracellular domain, residues 26-207
    Organism: Homo sapiens
    Gene Names: HLA-DRA1 Gene View for HLA-DRA
    UniProtKB: Search PDB | P01903   Protein Feature View
    Molecule: HLA class II histocompatibility antigen, DRB1-1 beta chain
    Polymer: 2 Type: protein Length: 190
    Chains: B
    Fragment: Extracellular domain, residues 30-219
    Organism: Homo sapiens
    Gene Name: Gene View for HLA-DRB1
    UniProtKB: Search PDB | P04229   Protein Feature View
    Molecule: HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine)
    Polymer: 3 Type: protein Length: 14
    Chains: C
    Organism: Influenza A virus (A/mallard/Sweden/S90391/2005(H3N8))
    UniProtKB: Search PDB | A8CDU0   Protein Feature View
    Molecule: Enterotoxin type C-3
    Polymer: 4 Type: protein Length: 240
    Chains: D
    Fragment: Residues 28-266
    Mutation: K70S, L72F, A73K, H74W
    Organism: Staphylococcus aureus subsp. aureus Mu50
    Gene Name: entC3
    UniProtKB: Search PDB | P0A0L5   Protein Feature View
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot

  •   Related Citations in PDB Entry (REMARK 1) Hide
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli bl21(de3)  
    Polymer: 2
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli bl21(de3)  
    Polymer: 3
    Scientific Name: Synthetic construct (Influenza A virus (A/mallard/Sweden/S90391/2005(H3N8)))   Taxonomy    
    Polymer: 4
    Scientific Name: Staphylococcus aureus subsp. aureus mu50   Taxonomy   Expression System: Escherichia coli  
  •   Related PDB Entries Hide
    Identifier Details
    1DLH   Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide (HA peptide) 
    1JWU   Crystal Structure of the Complex of the MHC Class II Molecule HLA-DR1 (HA peptide 306-318) with the Superantigen SEC3 Variant 3B1 
  •   Modified Residues Hide
    Identifier Formula Parent Type
    ACE C2 H4 O nonPolymer
    4DP C13 H15 N3 O4 TRP lPeptideLinking
  •   External Domain Annotations Hide
  •   Structural Biology Knowledgebase Data Hide
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Nguyen, T.T.,  Stern, L.J.

    Deposition:   2006-10-12
    Release:   2007-03-13
    Last Modified (REVDAT):   2009-02-24
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  •   Experimental Details Hide
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.30
    R-Value: 0.225 (obs.)
    R-Free: 0.224
    Space Group: H 3
    Unit Cell:
      Length [Å] Angles [°]
    a = 171.98 α = 90.00 
    b = 171.98 β = 90.00 
    c = 121.13 γ = 120.00