However, a potential S1-binding pocket was described for TbMCA2 and several residues were shown to be involved in substrate binding and/or enzyme activity [ 11]: Cys, Asp, Ser and Asp, which were found on α1, α1, L3 and L4, respectively (see Figures 2B and 3B).
Then, a binding pocket was generated.
A 10 Å sphere around the centre of the binding pocket was defined as binding pocket for the docking runs.
Furthermore, the physical binding environment of the binding pocket was evaluated using SiteMap [43, 44].
In addition, H334 residue that is structurally nearby the binding pocket was also examined.
First, the binding pocket was analyzed in the presence of the co-binding peptide using abacavir as the reference ligand.
The binding pocket was identified using Q-SiteFinder [46].
By using the built-in pocket finder, the binding pocket was identified.
Two spatial clusters of silencing mutations flanking the allosteric binding pocket have been described in [ 10].
There is no complete 3D structure for the 928 aa large protein but several binding pockets have been described (Fig. 1a).
