Is it good practice to remove bound proteins too?

[syedzayyan]

I am using these structures

https://www.rcsb.org/structure/6D9H
https://www.rcsb.org/structure/5N2S

And both of them contain bound things. 6D9H has a bound G - Protein, while 5N2S has a cytochrome attached. Is it necessary to remove them if we are drawing a binding box anyway?

[diogomart]

It depends on the system and on what you want to do. Reading about protein-protein interface inhibitors may (or may not) help you decide what to do.