[Chimera-users] Assembling 2 protein subunits into a heteromer

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 5 08:25:59 PDT 2022

> On Apr 4, 2022, at 11:32 PM, SANTOSH RAMA BHADRA RAO TATA <19807877 at students.latrobe.edu.au> wrote:
> Good evening, Meng,
> I'm trying to bind to protein subunits A and B with the stoichiometry of A-A-B-A-B pentameric form how can I do that in chimera? I have both A and B PDB files single chains. 
> Thanking you,
> With best wishes,
> Tata Santosh Rama Bhadra Rao,
> PhD Scholar,
> C/O Prof Helen Irving,
> La Trobe university,
> Bendigo, Vic-3550,
> Australia.
> Email: 19807877 at students.latrobe.edu.au; 
>             S.Tata at latrobe.edu.au
> Phone: 0499263974

The recommended address for Chimera questions is chimera-users at cgl.ucsf.edu CC'd here. 

Chimera doesn't predict how A and B would bind each other.  Instead you have to use any other information you might have.

 If there is a similar structure already known in pentameric form, then you could:

- open the known pentamer
- open the A structure 3 times and the B structure 2 times
- superimpose each of your structures on one monomer of the known pentamer, e.g. with matchmaker

See matchmaker (GUI tool or command) and other methods for superimposing structures:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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