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Figure 4.
Figure 4. Comparative analysis of V[NAR] loop topologies. (A)
Superimposed VMD[58] ribbon representations of V[NAR] domain
crystallographic structures. Expanded CDR3 protein backbone
traces are shown in ribbon representation for Type 2 V[NAR]s
1-A-7 (green; this study), 1-A-11 (red; this study), 12A-9
(cyan; PDB 2COQ), 12Y-2 (yellow; PDB 1VES), and the Type 1
V[NAR] HEL-5A7 (blue; PDB 1SQ2). (B) Licorice representations of
the 1-A-7 CDR3 loop highlighting the potential mimotope at
residues ^95SYP. (C) Ribbon representation of the 1-A-7 CDR3
(green) and CDR1 (yellow) loop regions in 180° rotation from
(B). Loop stabilizing interactions are shown as dotted lines.
(D) Licorice representations of the 1-A-11 CDR3 loop
highlighting the potential mimotope at residues ^93SYP. (E)
Ribbon representation of the 1-A-11 CDR3 (green) and CDR1
(yellow) loop regions in 180° rotation from (C). Loop
stabilizing interactions are shown, including the inter-loop
disulphide bond between Cys^29 and Cys^91.
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