[Chimera-users] Tetrahedral Sulphide bonds

Elaine Meng meng at cgl.ucsf.edu
Fri May 26 12:54:20 PDT 2017


Dear Yoga,
That is not really a Chimera question… maybe you can try searching some structure databases:

RCSB PDB search
<http://www.rcsb.org/pdb/secondary.do?p=v2/secondary/search.jsp#search_advanced-search>

There is also the Cambridge Structural Database for small molecules.
<https://www.ccdc.cam.ac.uk/>

Good luck,
Elaine

> On May 26, 2017, at 12:44 PM, Yogavel Manickam <myogavel at icgeb.res.in> wrote:
> 
> Dear Elaine,
> Recently I have determined this sulfide bond motif containing structure and I would like to know that any exiting PDB having this motif.
> Thanks
> Yoga  
> 
> ----- Original Message -----
> From: "Elaine Meng" <meng at cgl.ucsf.edu>
> To: "Yogavel Manickam" <myogavel at icgeb.res.in>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Sent: Friday, May 26, 2017 11:58:56 PM
> Subject: Re: [Chimera-users] Tetrahedral Sulphide bonds
> 
> Dear Yoga,
> What is the question?  Do you already have this structure?  What are you trying to do with Chimera?
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On May 26, 2017, at 10:21 AM, Yogavel Manickam <myogavel at icgeb.res.in> wrote:
>> 
>> Dear all,
>> Is there any example for tetrahedral sulphide bonds.
>> 
>>        CB-S1B (0.7)
>>        |1.8 A
>> CB-S2....S1A*...S3-CB
>>    2A  .   2A
>>        . 2A
>>        .
>>        S4
>>        |
>>        CB
>> 
>> 
>> S1 containing Cys adopt alternate conformation (S1A and S1B) with occupies of 0.7 and 0.3. 
>> 
>> S1A position occupied by Zn ion with ~0.7.
>> 
>> Any input will be appreciated.
>> 
>> Thanks
>> Yoga    
>> 




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