Figure 3

The predicted docking model of Stachyflin with the H5 HA of Ibaraki. Three-dimensional image of the HA trimer of Ibaraki was created based on the data from X-ray crystallography of A/Vietnam/1194/2004 (H5N1) (PDB code: 2IBX), and the sequence data of Ibaraki by homology modeling. (A) Residues colored in green indicate the region of the binding pocket for Stachyflin. The binding pocket is predicted to exist between helix A and helix D of the HA2 subunit and be surrounded by hydrogen bonds of D37-K121 and K51-T107, D37 to K51, and T107 to K121 residues in the HA2. (B) Binding position of Stachyflin in the binding pocket of the HA was predicted by docking simulation in Molegro Virtual Docker. The structure of Stachyflin is colored in yellow or orange and the residues constructing the binding pocket are in green. Two possible docking poses of Stachyflin with the HA were obtained, which are indicated as the positions of orange-colored Stachyflin (above) and yellow-colored Stachyflin (below) in the HA model. In the binding pocket, D37 may make a water-intermediate hydrogen bond with K121, and K51 may make a hydrogen bond with T107. (C) Dashed line indicates the salt bridge between D85 and K83 of another HA2 subunit. The distance between these residues was 2.55 Å.