Re: [ccp4bb] Unidentified ligand (electron density) found at active site

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Unidentified ligand (electron density) found at active site
From: gerrit {- at -} EMBL-HAMBURG {- dot -} DE gerrit {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2007-11-30

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Subject: Re: coot-bones not showing
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-12-01

Subject: Re: Unidentified ligand (electron density) found at active site
From: Gregg Crichlow gregg {- dot -} crichlow {- at -} YALE {- dot -} EDU
Date: 2007-12-01

I learned from an earlier CCP4BB post of a routine in Phenix that
searches a database of small molecules from (I think) 200 protein-small
molecule complex structures. Some of the small molecules seemed
redundant; however, they may be in different conformations in the
different structures that are used.
From the Phenix GUI, click on the "Strategies" menu, and then go to the
ligand sub-menu, and choose "ligand identification".

Gregg

***********************************
Gregg Crichlow
Department of Pharmacology
Yale University
Box 208066
New Haven, CT 06520-8066
***********************************

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Ronaldo Alves Pinto Nagem
Sent: Friday, November 30, 2007 7:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified ligand (electron density) found at active
site

Dear crystallographers,

I hope someone could give me a hint to solve this problem.
I have collected five datasets from the same protein and all of them,
including the highest resolution data set (1.6 angstrons), display at the
active site of the enzyme a very clear electron density with boundaries
well defined. The problem is that I have already tried to fit all kinds of
molecules present in the purification and crystallization conditions and
none of them fit well into the density.
Here are my questions: Is there any program available that could take a
small volume of the electron density map (obviously the unidentified
electron density ligand) and try to fit a list of known compounds (a list
that I do not have, by the way) for potential ligands? Or, is there any
website or program that could give me a list of compounds based only in
the backbone of the ligand I could sketch from the density (by backbone I
mean the plane shape of the compound â€“ I do not know its atom
composition)?

I hope someone could help.

Thanks

Ronaldo.

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: coot-bones not showing
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2007-12-01