If the ligand is a bona fide protein (more than a few amino acids and its own stable fold), I would include it under protein. However it is a matter of taste and, as Nat says, it will probably be dumped in the supplementary materials to be never looked at again.

Herman

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Nat Echols
Gesendet: Dienstag, 18. Februar 2014 17:29
An: [log in to unmask]
Betreff: Re: [ccp4bb] Table in NSMB

On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven <[log in to unmask]> wrote:

I'm filling out my table for NSMB, about a structure of protein ligand
bound to a receptor. They ask for 3 different lines regarding number
of atoms & bfactor. 1) Protein 2) Ligand/Ion 3) Water.
Does my protein ligand belong to Protein or  Ligand/Ion?

Why not list them each explicitly?  In my experience the recommended table of crystallography statistics for most journals is just a suggestion, not a strict format.  If you leave out information they might complain, but surely they won't object if you include additional details.  (They usually just exile it to the unformatted supplementary materials anyway.)

-Nat