[Chimera-users] reconstructing x-ray structure

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 27 16:52:45 PDT 2007

Hi Nevin,
I told Tom I would try to answer your question.

If I understand correctly, you have two structures (actually combined  
into one peptide chain in your example, 2gzv) but not a structure of  
their complex.  You would like to see the 4-residue peptide bound to  
expected binding site of the PDZ domain.

Sorry, but Chimera does not predict how structures bind each other or  
find favorable conformations of a single peptide chain.  You would  
first need to separate that structure into two different structures,  

(A) use some other program to predict how they bind each other.   
There are many "docking" programs that predict possible binding  
orientations given the structures of two molecules:  DOCK, Autodock,  
Glide, etc.
-- OR --
(B) if you already know or can guess how they should bind, you can  
open the two structures separately in Chimera and move them around  
into what you think is the correct position.  You can freeze/unfreeze  
structures (so that you can move only one at a time) with the Active  
checkboxes in the Model Panel (Favorites... Model Panel).

Other tools that might be useful while you are doing this are
- Find Clashes/Contacts
- Undo/Redo Move
- FindHBond

The last idea I have is that if there is some other structure of a  
PDZ domain bound to its peptide in the expected site, you could this  
PDZ domain and this peptide to the respective parts of the known  

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 27, 2007, at 3:33 PM, Z. Nevin Gerek wrote:

> I want to find out coordinates between peptide and protein. In x- 
> ray structures (such as: 2gzv it is a PDZ domain and peptide binds  
> to alpha helix in this domain), peptide is attached into C-terminal  
> of protein. At least they obtained bound structure with attaching  
> peptide into C-terminal of protein. Originally, peptide binds to  
> different place in the protein.
> Is there anyway to find the right place of peptide using this x-ray  
> structure in Chimera?
> If I find positions between peptide and protein, eventually i will  
> see peptide-protein interactions as in the right place.
> I hope this clarifies my problem.
> Nevin

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