You can superimpose the   homologous protein structures using PyMOL to better understand how structural conservation relates to substrate binding.Using PyMOL’s align and super commands, I superimposed protein structures based on their backbone atoms, minimizing RMSD and highlighting conserved folds and active-site geometry:Once the structures were aligned, the sequence alingment file of the superimposed structure is used to look at the conservation of the substrate binding site using differnt tools like Clutal Omega, Muscle, KA align and other tools.To visualize conserved regions—especially around the substrate-binding ESPript is used which integrates sequence alignment with secondary structure annotation. This makes it much easier to pinpoint conserved amino acids that are likely critical for substrate recognition and catalytic activity.This combined structural and sequence-based approach provides valuable insights into how proteins maintain function despite sequence variation.