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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 4. Detailed comparison of the particular amino-acid residues in the peptide-binding grooves between BF2*0401 and BF2*2101.

Figure 4

(A and B) Pockets C, D and E of the peptide-binding grooves in BF2*0401-IE8 (A) and BF2*2101-11mer (B), respectively, are highlighted, showing the size differences, with the amino-acid residues with different side chains labelled on the surfaces. (C) Superposition of the Cα-traces of the α1 and α2 domains in BF2*0401 (red) and BF2*2101 (green), with the α1 helix fixed. (D) Side chains of the amino-acid residues contributing to the binding groove in BF2*0401 (pink) are relatively larger than their counterparts in BF2*2101 (cyan). (E) Interactions of Arg9 with the peptides in BF2*0401-IE8 (pink), BF2*2101-10mer (orange) and BF2*2101-11mer (cyan), showing Arg9 in BF2*0401-IE8 adopts a fixed conformation, unlike in BF2*2101 where the unusually-large cavity makes Arg9 mobile. The peptides are viewed with the α1 helices fixed. Salt bridges formed between Arg9 and peptide are shown as dashed lines in pink for IE8, orange for 10mer and cyan for 11mer. (F) Conformation of Arg9 with constrained space in BF2*0401-IE8 (pink), compared to those in BF2*2101-10mer (orange) and BF2*2101-11mer (cyan). Side chains of residues around each Arg9 are labelled and shown as sticks; clearly shown are bulky side chains in BF2*0401.