HEME protein docking with small ligand using HADDOCK 2.4

Dear HADDOCK community,

I am trying to perform a docking between a multiheme protein and a small ligand. This protein has 10 C-type hemes coordinated by two His as axial ligands each.

I have verified in an ASCII text editor that formatting of the PDB was correct, and the structure looks good both in a PDB visualizer (ChimeraX) and in the visualizer implemented in HADDOCK: Cys are covalently bound to the HEC residue and the NE2 atom of HIS are in close range with the heme Fe.

After the docking: (i) Cys do not seem to remain bound; (ii) His become protonated at the NE2 atom, which seems to cause the hemes to be displaced far apart from the starting structure.

I have run the Docking in EASY mode, and selected last 150 residues as active, as we have limited experimental data on this system yet.

Do you know what could be the reason of this behavior? Maybe there is something wrong in the PDB file that leads to not identifying the heme properly as a covalently-bound protein cofactor? Would a change of docking parameters make a difference, like for instance limiting any part of the simulated annealing?

I would be pleased to send you the PDBs to your email if interested, but I was not able to upload these to the post as I am a new member in the community.

Thank you all for your collaboration.


We do support heme B and heme C - see HADDOCK Web Server - Settings

You can download example PDB files for those if you want to check the naming

Other hemes can be handled as well as ligands, but no patches will be applied (e.g. to create a covalent bond).

As for the HIS, provided you have expert level access, you can manually define their protonation state.