Write two incoming molecules as a single entry to a PDB file

I have a workflow where one molecule (the ligand) is coming from a SDF file and another (the protein) from a PDB file. I would like to correctly write them both to a PDB file so that it is formatted as a single entry rather than two separate molecules; the molecules are part of the same system. As close as I have gotten, is to use aggregate fragments, but while it writes a single entry, the connection table is not correct.