The peptide-binding structure consist of a membrane-distal groove formed by two anti pararel α-helices overlaying and eight-strand ß-sheets. In the case of HLA class I, the groove corresponds to a contiguous amino acid sequence formed by the N-terminal region of the single HLA-encoded subunit, or heavy chain, while for HLA class II, it is formed by the juxtaposition of the N-terminal regions of two HLA-encoded α- and β- chains. A significant difference is that for HLA class I the peptide is confined by binding groove interactions at both the N- and C-termini while for HLA class II, each end of the peptide can overhang the binding groove.
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