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CCP4BB <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, March 7, 2022 9:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand binds to one molecule
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Hi folks
Just my two ha’porth; if you go back
MacCHESS, Cornell University
>> schul...@cornell.edu
>> From: CCP4 bulletin board on behalf of Palm,
>> Gottfried
>> Sent: Sunday, March 6, 2022 4:10 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb]
@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] ligand binds to one molecule
Dear all,
I don't think, there is much to add to the statement of Bernhard or
James that different protomers in the asymmetric unit (must) have some
difference in there contacts and therefore often in their
conformation. Wh
Well, there is almost nothing left to suggest, but one. Try co-crystallizing.
While in solution molecules will have more flexibility to adopt a conformation
that fits ligand bound state better. When soaking there might be restrictions
on conformational changes needed for better binding due to al
behalf of Palm, Gottfried
Sent: Sunday, March 6, 2022 4:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] ligand binds to one molecule
Dear all,
I don't think, there is much to add to the statement of Bernhard or James
that different protomers in the asymmetric unit (must) have
Dear all,
I don't think, there is much to add to the statement of Bernhard or
James that different protomers in the asymmetric unit (must) have some
difference in there contacts and therefore often in their
conformation. What it doesn't answer is a chicken or the egg question:
do the differe
As you stated, you have multiple protomers in the asymmetric unit, where they
are free from
crystallographic symmetry constraints. Generally that means different local
environment for
each protomer. Inspecting the sites in the different protomers (frequently
related by various
non-crystallogra
Hey,
That is a good question, and there could be multiple reasons. One
possibility could be the crystal contacts. I have experience with the
pentameric vial surface protein (PMID: 24648448), and I could see the
carbohydrate ligand only in a subset of protein chains in ASU.
Another reason could be
Perhaps the subunits have different conformational states that are differently
able to bind the ligand. There are definitely oligomers where the subunits do
that e.g. mGluR1 binding domain dimer is usually 1 open subunit and 1 closed in
the active state without cations at the interface. This is
