Hi Matthias,
Thank you for response. Could you provide one or more pdb codes as example?
Best,
Christian
------------------------------------------------------------------------
*From:* Barone, Matthias <bar...@fmp-berlin.de>
*Subject:* [ccp4bb] ligand bound to only one chain in the crystal
*Date:* Tuesday, October 27, 2020, 12:55
*To:* CCP4BB@JISCMAIL.AC.UK; Christian GALICIA
Hi Christian
One of our proteins crystallizes always as non-crystallographic dimer.
We occasionally find inhibitors bound to a second non-canonical site.
Usually, the inhibitors bound to the second binding sites are
sufficiently resolved only on one of the protein dimer. In these cases
I often fail to place the second inhibitor at all and have to leave an
unmodeled blob there. To exclude that this second binding site is not
a crystal artifact, we used NMR HSQC to show that chemical shifts
perturbations do occur even in solution and low inhibitor excess.
Best, Matthias
Dr. Matthias Barone
AG Kuehne, Rational Drug Design
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Christian GALICIA <christian.galicia.diaz.sant...@vub.be>
*Sent:* Tuesday, October 27, 2020 11:19:23 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] ligand bound to only one chain in the crystal
Hello,
In our structure only one chain in a crystallographic trimer
(non-biological) shows a ligand bound to it (with clear density).
There doesn't seem to be any channels (or lack of them) favoring that
specific site. Can the community give your opinion on whether this can
make the presence of the ligand or its biological role questionable,
and give any examples of similar cases you might be aware of. Thank you.
--
*Christian Galicia*
Post Doctoral Scientist
E-mail: cgali...@vub.be <mailto:cgali...@vub.be>
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