Figure 4
From: Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity
Comparison of Mitsuba with Threefoil. (a) Sequence alignment of Mitsuba-1 with related β-trefoils. The secondary structure elements of Mitsuba-1 (detected automatically) are shown as arrows and coils. The PDB entries for Threefoil and Ct1 are 3PG0 and 3VSF respectively. The N-terminal catalytic domain of Ct1 is omitted. Mitsuba-1 shows 29% sequence identity to Threefoil, and only 22% to Ct1. Threefoil shows 48% sequence identity with the Ct1 trefoil domain. The figure was drawn using ESPRIPT58. (b) A stereo ribbon diagram of the first subdomain of Mitsuba-1, shown in purple. The central cavity of the protein is shown as a translucent grey surface. Threefoil (shown in pink) has several mutations compared to Mitsuba-1 in the central region, and the notable mutations are shown as sticks and labelled. Threefoil has Trp 42 (and two equivalents in the other subdomains) in place of Phe 42 of Mitsuba-1. This larger side-chain is accommodated by Gln 78 and the altered backbone structure nearby, but Leu 80 of Mitsuba-1 would clash with the tryptophan. The hydrophobic core of Threefoil is also filled by Leu 16; replacements at positions 7 and 29 on either side of this side-chain allow better packing, leaving no significant cavity. Cavity analysis was performed with KVFinder25.
