Yes, the easiest way to do it is using pymol.

Yeah, in Pymol pretty easy:

Load the PDB file in Pymol:

> remove solvent (too many waters)

> remove polymer.protein (now you just have the ligand)

Maybe you just want the protein though

remove not polymer.protein (now you just have the protein)

Save the PDB files using the mouse.

The ligand has a 3 letter name in the sequence view, but usually if you just "select organic" then you have the ligand.

Either from Pymol, or open the pdb file with a text editor and manually delete the lines corresponding to the atom coordinates of your ligand and save the file again