Dear wei,
i think you have to keep in mind what do you have in your cristal
growing condition, and in you protein buffer.
Because maybe you can find which molecules this ligand could be.
It's difficult to help more, because we don't know you level of sigma
for the map and the resolution of your dataset.
But in all case, if you have an idea of what it could be, and you don't
find restraint and molecules in existing library, you can use "monomer
library sketcher" in ccp4 to sketch manually your molecule, and generate
library of restraints.
Hope to help you.
Nicolas
Le 16/07/13 17:56, Oganesyan, Vaheh a écrit :
It actually looks much like pyrophosphate! If your protein is
phosphatase and the extra density is in vicinity of the active site it
might be the remaining product of reaction.
/*/Vaheh/*/
------------------------------------------------------------------------
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
Of *Bosch, Juergen
*Sent:* Tuesday, July 16, 2013 11:53 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Dose anyone see this ligand before?
Special position ?
sulfate-size ?
Jürgen
On Jul 16, 2013, at 11:35 AM, Wei Feng wrote:
Dear all,
I found some redundant density in my structure beween two molecule.
(see picture 1 and 2)
But I am not sure which ligand will be.
Dose everyone see this ligand before? If so, can you tell the PDB code
or send me the struture file?
Thank you for your time!
Wei
**
<picture1.jpg><picture2.jpg>
......................
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-2926
http://lupo.jhsph.edu
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