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: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-11-30

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

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

If you can narrow down the possibilities of compounds to a list of a few - let's
say not more than 20...30 - then ARP/wARP 7 might be of help. It has a ligand
building tool. One of its protocols is building an unidentified ligand from a
list. Check the user-guide for detailed information on the usage.

Regards,
Gerrit.

> 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 navigation

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

Previous message:
Subject: Re: Unidentified ligand (electron density) found at active site
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-11-30

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