1
$\begingroup$

Problem

Using WinCoot or SWISS PDB viewer, how would one merge monomeric structures that should be in dimer formation?

What I have done:

  1. I have downloaded the PDB-file which shows the monomer with a bound drug (Infliximab Fab fragments), but it should be a trimetric structure as whole -although you only get the monomer when you download the file (TNFa) .
  2. I have opened the file in both coot and SWISS-PDB viewer, and opened three copies of the monomer, but they just overlap and I am not able to combine them to the proper structure

I also know that it is possible to download the "biological assembly" PDB-file that has the entire trimetric structure, but the point here is to be able to do that on my own (which should be easy for those who know it?).

I am very new to all of this modeling, so there might be something basic I don’t understand. But I though that you can somehow "merge" the monomers by using some "layer" function? I am really unsure.

$\endgroup$

closed as off-topic by Martin - マーチン Dec 10 '15 at 6:11

  • This question does not appear to be about chemistry within the scope defined in the help center.
If this question can be reworded to fit the rules in the help center, please edit the question.

  • $\begingroup$ Uh, I vote to leave this open for now; I fail to see how it's a HW question. $\endgroup$ – M.A.R. Dec 9 '15 at 16:52
  • $\begingroup$ Well, it's debatable, but OP should show some research effort and knowledge about these programs. BTW @H.T. Do you simply want to have coordinates duplicated or find "real" dimer? $\endgroup$ – Mithoron Dec 9 '15 at 18:32
  • $\begingroup$ I think I simply want to have the coordinates duplicated - but not just overlapped (in the sense that its a trimeric structure, but I only have one monomer). I am very new at this (modelling), so I will rephrase my question a bit and remove the homework tag (its a course assignment). $\endgroup$ – CuriousTree Dec 9 '15 at 19:27
  • $\begingroup$ cross-posted biology.stackexchange.com/questions/41338/… $\endgroup$ – Mithoron Dec 9 '15 at 20:56
  • $\begingroup$ I am closing this question because the cross-posted version is more elaborate. $\endgroup$ – Martin - マーチン Dec 10 '15 at 6:11
1
$\begingroup$

The PDB-file only contains the asymmetric unit, and no information on a potential biological relevant multimer. So you will need to get information about the state in solution experimentally.

That being said, one can often deduce from the size of the contact surface whether you have a potential quarternary structure. You can do this by hand, but the PISA-server is quite helpful there, and it will also output the multimer PDB-file:

http://www.ebi.ac.uk/pdbe/pisa/

If you just want to apply symmetry operators to your asymmetric unit in order to create symmetry mates, you can do so in

Pymol:
- click Action/generate/symmetry mates/within X Å
- from the command line:
        symexp prefix, selection, cutoff
        , e.g. symexp sym,1GVF,(1GVF),5
   see also http://pymolwiki.org/index.php/Symexp

Coot:
- if you just want to look at the symmetry mates, activate View/Cell&Symmetry with an appropriate radius and/or select "Symmetry by molecule"
- if you would like to actually create the symmetry mates, try Extensions/Modelling/New Molecule from Symmetry Op  - however you will have to specify the SymOp manually.

You will need to have the CRYST1-record in your PDB-file with the correct space group.

$\endgroup$

Not the answer you're looking for? Browse other questions tagged or ask your own question.