(a)
(b)
Figure 9. Ramachandran plot for (a) the homology model and (b) the 5XW4 template. The plot displays the phi and psi angles of amino acid residues, which demonstrate rotations around the N- Cα (phi) and Cα -C (psi) bonds. Green and orange outlines indicate regions that are sterically favourable conformations. To understand the structural properties that allow for substrate and inhibitor recognition of Cdc14 in A. alternata , a homology model was created in MOE using the target sequence from A. alternata and a template entry from 5XW4. The homology model and the template sequences were then realigned and superposed, with the backbones coloured by the Root Mean Square Deviation (RMSD) (figure 7). Structures were aligned based on sequence similarities and structural characteristics to achieve the optimal positioning of protein residues and superposed to maximize the overlap between structurally similar regions. Ramachandran plots were generated and compared between the homology model (figure 8a) and the template (figure 8b) to ensure that the predicted structure of Cdc14 in A. alternata aligns with the known structure. The two plots demonstrate high similarity in the distribution of phi and psi angles, with most points concentrated in the two green regions in Quadrants II and III, which correspond to the alpha helices and beta sheets. In comparison to the template, the homology model has several additional points scattered in the orange region, which represents a less favoured allowed region. It also shows three residues – Val368, Ala82, Gln40 – in the disallowed region, whereas the template shows one (Val321).
Figure 10: Overall view of the 5XW5 (yeast Cdc14 phosphatase in complex with a peptide) ligand chain in the model active site.
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