Dear all,
I am working on a membrane protein covalently bound to a molecular
antanna: it is known that this molecule binds to lysine residue but I do
not know how many and which lysine residues it binds. 20 diffraction
datasets of this protein-ligand complex have been obtained and now, I
would quickly localize the ligand using the Fo-Fc map of each data set
and using the information on the covalent bound protein-ligand.
Ligandfit tool (PHENIX) seems to be indicated to do this; to use the
information on the covalent bound, I am using the ligand_start keyword
with a pdb containing a ghost atom (however present in ligand model)
perfectly superposed to the lysine atom that should bind the ligand.
The command used is:
phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb
ligand_start=lig_start.pdb input_labels="FOFCWT PHFOFCWT" \
refine_ligand=True \ nproc=32 \ cif_def_file_list=lig.cif
description:
- prot.mtz (data)
- prot.pdb (protein without ligand)
- lig.pdb (ligand containing ghost atom)
- lig_start.pdb (ghost atom superpose to NZ of a lysine)
- lig.cif (restrain of lig.pdb)
Strangely, no ligand is found at the end of the process even reducing
ligand_cc_min to 0.01. I have run the same command by using an other
protein where an other ligand has been correctly fitted but, also in
this case, no ligand has been detected. Conversely, without the use of
ligand_start, ligandfit properly localizes the ligand.
I'm doing some mistake in the use of ligand_start? Do you know an
other tool to perform a ligand fitting in these conditions?
Thanks for your answers.
Danilo
