Figure 6. Interactions between DrPOMK and GalNAc-β3-GlcNAc-β4-Man.
(A) Surface representation of DrPOMK in complex with Mg2+ ions, ADP, AlF3, and GalNAc-β3-GlcNAc-β4-Man. The same coloring scheme as in Figure 3 is used. (B) An enlarged image of the GalNAc-β3-GlcNAc-β4-Man binding region showing the detailed molecular interactions important for the trisaccharide recognition. DrPOMK residues C201, D202, C241, G242, and H243 have both main chains and side chains shown as sticks, while the rest residues only have side chains depicted. Hydrogen bond interactions are shown as dashed lines. The linkages in the trisaccharide and the Man-O6 group are indicated.
Figure 6—figure supplement 1. Electron density of Mg/ADP/AlF3 and GGM-MU.
(A) Fo-Fc difference electron density map at 2.5 σ shown as green wires before Mg/ADP/AlF3 are modeled in the structure. DrPOMK is shown as white ribbons. (B) Fo-Fc difference electron density map at 2.5 σ shown as green wires before the GGM-MU molecule is modeled. The electron density corresponding to the MU moiety is significantly weaker compared to that of the GGM trisaccharide, consistent with our NMR results showing that the MU group is flexible and does not contribute to binding to POMK (Figure 5—figure supplement 1).