I want to dock homo-pentameric nanobody.
i have CDR information of nanobody but don’t know the antigen’s binding site should i on this option “Automatically define surface residues as passive” after that continue the multibody docking tutorial?
i have modelled the structure with alpha fold does it necessary to renumber the nanobody and antigen?
and please share any other requirement for this!
Thankyou in advance
Hi! I imagine you want to dock a nanobody to a pentameric protein, correct?
defining the surface of the antigen as passive is OK in this case, but please have a look at this to define the docking parameters HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver – Bonvin Lab (scenario 1)
if your target antigen is a pentamer you may need to assign the same chain ID to the antigen PDB file, renumbering the residues (similarly to what is done in the tutorial for the antibody). In this way HADDOCK will understand that the pentamer is a unique entity.
the alphafold nanobody should be fine!
Cheers!
Thankyou marco.giulini for explaining.
Little correction; my target antigen is monomer so I have to dock 5 antigen with a Homo-Pentameric nanobody.
Also I have separated my antigen from a heterodimer because nanobody is specific for a single unit of that heterodimer, is it necessary to renumber that antigen?
Or any other preparation needed please specify?
OK, now I understand! In this case you can avoid the antigen renumbering, the Alphafold structure should be fine.
Additionally, I imagine that the complex will be symmetric for all the five antigens, so you could in principle dock only one nanobody subunit to the desired antigen and then use the same interface in the other subunits.
Means, i will have to dock one by one for each unit of nanobody (like i will have to upload pentameric nanobody and one antigen at a time and specify CDRs for one unit. After that i will have to upload that cluster(got from first docking) again and dock second subunit and so on…?)
Or upload 6 pdbs (1 Penatmeric nanobody, 5 antigen ) in one go?
Does it require to renumber that nanobody?
it means that you could dock only one nanobody subunit to one antigen (two-body docking, faster and more likely to be successful) and then take the best model and replicate it in the remaining four subunits (without doing the docking again).