Structural Homology and Protein-Substrate Docking of BAAI

Homology model was constructed for BAAI with the L-AI of E. coli (ECAI) (PDB ID: 4F2D) as a template by SWISS-MODEL (Waterhouse et al., 2018) using default parameters. The Ramachandra plot of model was examined by PROCHECK (Laskowski et al., 1993) to ensure the amino acid residues were not situated in unfavorable region. Protein-substrate docking of BAAI with various substrates were performed using AutoDock Vina software (Trott and Olson, 2009). The interacting amino acid residues of BAAI with ligands were visualized and highlighted using PyMOL software (DeLano, 2002) and Discovery Studio visualizer (Version 17.2.0.16349, San Diego Dassault Systems).