This is a groove formed between the alpha helices of the a 1 and a 2 domains. The floor of the groove is composed of beta sheets derived from the same domains. A wide, and 11 A deep. If this groove acted as the lock in the very common lock and key model of many proteins, each MHC molecule could only bind to a single selected peptide. A pocket is defined as the unit having an affinity for a corresponding peptide side chain.
Some pockets have a well-shaped structure with an affinity for only one side chain.
Other pockets have an affinity for a group of side chains, and sometimes the boundaries between the pockets are not clear. In order to locate the pockets of this molecule s binding groove, Matsumera et al. They were not only able to locate these pockets, but also find their varying depths. Six pockets, designated as A through F , were found. A , B , C , and F are considered deep pockets.