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. Author manuscript; available in PMC: 2016 Sep 11.
Published in final edited form as: J Immunol. 2012 Oct 5;189(9):4478–4487. doi: 10.4049/jimmunol.1200885

Figure 2. The peptide-binding groove of BF2*0401.

Figure 2

Comparison of the peptide-binding grooves between BF2*0401 and BF2*2101, illuminating an extremely narrow groove of BF2*0401 and an unusually large binding groove in BF2*2101. (A-C) Molecular surfaces (grey) of the peptide-binding grooves of BF2*2101-11mer (A), BF2*0401-IE8 (B) and BF2*2101-10mer (C) with the peptides (11mer, IE8 and 10mer coloured in cyan, pink and orange, respectively). The N- (P1) and C- (P11, P8, and P10) termini of the peptides are marked. Pockets in each groove are sequentially labelled A to F. (D and E) The surface of BF2*0401-IE8 binding groove is superimposed onto that of BF2*2101-11mer (D) or BF2*2101-10mer (E). BF2*0401 is shown in pink, while BF2*2101-11mer and BF2*2101-10mer are coloured in cyan and orange, respectively. (F) Structure-based amino acid sequence alignment of the α1-α2 domains of BF2*0401 and BF2*2101, with the secondary structure elements indicated above. The cysteine residues involved in the first disulfide bond are marked by green 1. Conserved residues are high-lightened in red. Residues forming the binding groove are marked by orange stars for BF2*0401 and blue stars for BF2*2101.