Fig. 3.

Binding of monofucosyl ABH family HBGAs to the 2004 P domain dimer. (A) Surface representation (top view) showing a close-up view of one of the two binding sites in the 2004 P domain dimer bound to an A-type trisaccharide. Identical interactions with the trisaccharide were observed for the other binding site of the dimer and are not shown. Amino acid residues in site 1 and site 2 are shown in pink and green, respectively, with other residues from the dimeric subunits in the vicinity shown as blue and cyan. The HBGAs, here and in all subsequent figures, are shown as yellow sticks, with nitrogen atoms and oxygen atoms shown in blue and red, respectively. The individual saccharide moieties in the A-type trisaccharide are labeled as Fuc (fucose), βGal (galactose), and GalNAc (N-acetylgalactosamine). (B) Detailed interactions of the A-type trisaccharide with the 2004 P domain dimer. P domain residues participating in the hydrogen-bonding (black dashed lines) and hydrophobic (red dotted lines) interactions with the trisaccharide are labeled and shown as pink sticks, with nitrogen and oxygen atoms in blue and red, respectively; the rest of the dimer is shown as a cartoon representation. The individual moieties of the trisaccharide are labeled as described above (A). The water molecule involved in solvent-mediated interactions with site 2 is labeled W and is shown as a red sphere. (C) Surface representation (top view) showing a close-up view of one of the two binding sites in the 2004 P domain dimer bound to the H-type pentasaccharide. Amino acid residues in site 1 and site 2 are colored as described above (A). The H-type pentasaccharide is shown as stick model with individual moieties labeled as Fuc (fucose), βGal (galactose), GlcNAc (N-acetylglucosamine), and Glc (glucose). (D) Detailed interactions of the H-type pentasaccharide with the 2004 P domain. P domain residues participating in the hydrogen-bonding (black dashed lines) and hydrophobic (red dotted lines) interactions with the pentasaccharide (individual moieties labeled as described above) are labeled and shown as pink sticks, with nitrogen and oxygen atoms in blue and red, respectively. The individual moieties of the pentasaccharide are labeled as described above (C).