Class II MHC protein. A class II MHC protein consists of homologous α and β chains, each of which has an amino-terminal domain that constitutes half of the peptide-binding structure, as well as a carboxyl-terminal immunoglobulin domain. Notice the trough-like peptide-binding site, which is similar to that in class I MHC proteins except that it is open at both ends, allowing class II MHC proteins to bind longer peptides than those bound by class I.

[Drawn from 1DLH.pdb.]