PDBe 2ipk

X-ray diffraction
2.3Å resolution

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

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Enterotoxin type C-3 Chain: D
Molecule details ›
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
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DR alpha chain Chain: A
Molecule details ›
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
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DRB1-1 beta chain Chain: B
Molecule details ›
Chain: B
Length: 190 amino acids
Theoretical weight: 22.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04229 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Sequence domains:
Structure domains:
Hemagglutinin Chain: C
Molecule details ›
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%)

Ligands and Environments

No bound ligands

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: R3
Unit cell:
a: 171.98Å b: 171.98Å c: 121.129Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.203 0.224
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21(DE3)
  • Not provided