Several different peptides have been complexed to the the membrane protein, MHC. As is shown here, there is both an alpha and beta chain, which are not covalently attached. Two sections of the alpha domain form the binding cleft, which can accomodate peptides that are 8-11 residues in length. Performing an MD simulation with periodic boundary conditions (PBC) of the entire solvated system will be too computationally intensive with the available resources. Therefore, the system must be truncated.

We will examine the complex crystallized with the four letter PDB code of 2vaa, which can be downloaded from the RCSB website.