Hexamer transmembrane

HADDOCK
1

I have already seen the question related to dimers and how to manipulate them, I used pdb tools on a hexamer ,and i don’t see the structure of the protein anymore. is it possible to dock with hexamers and if yes, what should I do in order to ensure a better result and make it easier for the software? thankyou

2

Dear user,

I am not sure I understand your question.

Could you please clarify if:

  • you want to perform the 6-body docking (hexamer)
  • you want to perform docking of an other bio-molecule on a hexameric complex you already have
3

In principle, pdb_tools can handle hexamers. Try to apply a single pdb_tools function at a time and examine the output to determine the source of error.

For the multi-body docking, it is important for each individual molecule to have a unique chain id. Check out this multi-body docking tutotial, if you’re using HADDOCK2.4 web

4

yes sure, I wanted to dock a trimer with a transmembrane hexamer , at last I was able to renumber the residues , and I specified the active residues also, it was a bit restricted , but i managed to split into two dockings , I would be glad to hear still if you have any advice or suggestions regarding this type of docking, Thank you :heart_hands:

5

I did , and it worked at last, Thank you for your reply, and I will check the suggested tutorial.:smiling_face:

6

If I understand well, this is a two body docking problem.
For this you need:

  • to define the hexamer as a single chain (e.g. A), and make sure all residues have different index (pdb_chain -A hexamer.pdb | pdb_reres -1 > hexamer_ready.pdb)
  • to define the trimer as an other single chain (e.g. B) and make sure (as well) that all residues have a different index within the same chain (pdb_chain -B trimer.pdb | pdb_reres -1 > trimer_ready.pdb)

With these inputs, you should be able to perform the docking.