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. 2009 Jan 9;4(1):e4164. doi: 10.1371/journal.pone.0004164

Figure 1. The Peptide Binding Region (PBR) of the Major Histocompatibility Complex Class II.

Figure 1

HLA-DRβ1*1501 molecule showing the α-chain as a pink ribbon and the β-chain as a light blue ribbon. (A) Frontal view and (B) top view. The amino acids defining each pocket are represented as balls according to their size in a different color: Pocket 1 (magenta), Pocket 4 (dark blue), Pocket 7 (gray) and Pocket 9 (green). Maximal Speed Molecular Surface representation (www.scripps.edu/~sanner/html/msms_home.html) [37] (C) Frontal view evidencing the trough of the PBR and (D) Top view showing the deep pockets P1 and P9 whereas Pocket 4, 6 and 7, more superficial, lye towards the walls of the groove. These figures were made using the VMD software [24].