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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

X-ray diffraction
2.3Å resolution
PDB entry 2ipk coloured by chain, front view.
PDB entry 2ipk coloured by chain, side view.
PDB entry 2ipk coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetramer
Accessible surface area: 28328.44 Å2
Buried surface area: 9183.91 Å2
Dissociation area: 723.93 Å2
Dissociation energy (ΔGdiss): -3.12 kcal/mol
Dissociation entropy (TΔSdiss): 13.06 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-108597

Macromolecules

HLA class II histocompatibility antigen, DR alpha chain
Chain: A
Length: 183 amino acids
Theoretical weight: 21.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01903 (Residues: 26-207; Coverage: 80%)
Gene names: HLA-DRA, HLA-DRA1
Pfam:
InterPro:
CATH:
SCOP:
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2ipk, assembly 1, front view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2ipk, assembly 1, side view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2ipk, assembly 1, top view.
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HLA class II histocompatibility antigen, DRB1 beta chain
Chain: B
Length: 190 amino acids
Theoretical weight: 22.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01911 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Pfam:
InterPro:
CATH:
SCOP:
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2ipk, assembly 1, front view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2ipk, assembly 1, side view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2ipk, assembly 1, top view.
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Hemagglutinin
Chain: C
Length: 14 amino acids
Theoretical weight: 1.63 KDa
Source organism: Influenza A virus
Expression system: Not provided
UniProt:
  • Canonical: A8CDU0 (Residues: 59-71; Coverage: 13%)
Hemagglutinin in PDB entry 2ipk, assembly 1, front view.
Hemagglutinin in PDB entry 2ipk, assembly 1, side view.
Hemagglutinin in PDB entry 2ipk, assembly 1, top view.
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Enterotoxin type C-3
Chain: D
Length: 240 amino acids
Theoretical weight: 27.85 KDa
Source organism: Staphylococcus aureus subsp. aureus Mu50
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0L5 (Residues: 28-266; Coverage: 100%)
Gene name: entC3
Pfam:
InterPro:
CATH:
SCOP:
Enterotoxin type C-3 in PDB entry 2ipk, assembly 1, front view.
Enterotoxin type C-3 in PDB entry 2ipk, assembly 1, side view.
Enterotoxin type C-3 in PDB entry 2ipk, assembly 1, top view.
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