Abstract

Neisseria gonorrhoeae is the cause of sexually transmitted diseases. Binding to the host cells by type IV pili (Tfp), it has role in motility, fruiting body formation, DNA transformation, and host cell attachment. Nevertheless, pili has other unknown roles as well. Investigating the proteins’ tertiary structure via bioinformatics instruments could assist to recognize their functions as well as interactions with other compounds via applying less cost and time. The current study deals with better identify and determine the 3D structure of ligand-binding site and PilT in N. gonorrhoeae using bioinformatics instruments. Moreover, assessing the surface available pockets, clefts, and single-scale amino acid features were considered. The most proper model of PilT was designed by SWISS-MODEL software, and the consequent epitope mapping processes were used to determine Ps2v2 and critical residues. Five pockets have been found by GHECOM server on protein surfaces utilizing mathematical morphology. The pockets of active sites and small-molecule-binding sites were greater compared with the average value. The active site values were much greater indicating that pockets have role in predicting the active sites and binding sites from the protein structures. Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.