Yes, many proteins have transitional global arrangements that it traverses as it meets some goal. For example, kinesin and dynein walk along microtubules in a w

Yes, many proteins have transitional global arrangements that it traverses as it meets some goal. For example, kinesin and dynein walk along microtubules in a way where we could never perfectly characterize the intermediary states since it's effectively a motor with free rotation around certain elements. A lot of crystallography is focused on enzymatic reactions where you bind a ligand that sits there for the sake of introducing some conformation that you can study. The ligands generally approximate the natural substrate at either the beginning, end, or some intermediate step in enzyme catalyzed synthesis.