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Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation

X-ray diffraction
2.72Å resolution
PDB entry 3pgd coloured by chain, front view.
PDB entry 3pgd coloured by chain, side view.
PDB entry 3pgd coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero trimer
Accessible surface area: 17820.19 Å2
Buried surface area: 7348.15 Å2
Dissociation area: 1,221.59 Å2
Dissociation energy (ΔGdiss): 18.79 kcal/mol
Dissociation entropy (TΔSdiss): 8.82 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135318
Assembly 2
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Multimeric state: hetero trimer
Accessible surface area: 17941.69 Å2
Buried surface area: 7433.18 Å2
Dissociation area: 1,207.75 Å2
Dissociation energy (ΔGdiss): 17.83 kcal/mol
Dissociation entropy (TΔSdiss): 8.82 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135318

Macromolecules

HLA class II histocompatibility antigen, DR alpha chain
Chains: A, D
Length: 193 amino acids
Theoretical weight: 22.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01903 (Residues: 26-217; Coverage: 84%)
Gene names: HLA-DRA, HLA-DRA1
Pfam:
InterPro:
CATH:
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 3pgd, assembly 1, front view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 3pgd, assembly 1, side view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 3pgd, assembly 1, top view.
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HLA class II histocompatibility antigen, DRB1 beta chain
Chains: B, E
Length: 199 amino acids
Theoretical weight: 23.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01911 (Residues: 30-227; Coverage: 84%)
Gene name: HLA-DRB1
Pfam:
InterPro:
CATH:
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 3pgd, assembly 1, front view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 3pgd, assembly 1, side view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 3pgd, assembly 1, top view.
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Class-II-associated invariant chain peptide
Chains: C, F
Length: 15 amino acids
Theoretical weight: 1.73 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P04233 (Residues: 106-120; Coverage: 5%)
Gene names: CD74, DHLAG
Class-II-associated invariant chain peptide in PDB entry 3pgd, assembly 1, front view.
Class-II-associated invariant chain peptide in PDB entry 3pgd, assembly 1, side view.
Class-II-associated invariant chain peptide in PDB entry 3pgd, assembly 1, top view.
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