Dear all, the tenor seems to be, if you see the ligand in any of the monomers, that's the mode the ligand binds. We have seen other cases, though, too.
Usually the protein I am thinking of (TetR(D)) crystallizes with one molecules /a.u. In solution it is an obligate dimer. The dimer is formed by a crystallographic axis. Each chain binds one ligand and for wt the binding constant is sub uM without noticable cooperativity. For some mutants we saw breakdown of this crystallographic axis (symmetry dereases from I4(1)22 to P4(3)2(1)2), though, and now one of the chains harbored a ligand, the other did not. It took some very careful measurements to check that these mutants bind the ligand anticooperatively, i.e. the first chain binds a ligand, the second of the monomer so much weaker that we couldn't measure it. So, in case of oligomers, keep cooperativity in mind. Greetings Gottfried On Tuesday, 27-10-2020 at 12:57 Ian Tickle wrote: Hi Christian I wouldn't worry: if the density is clear that nails it. You didn't say whether this is a soak or co-crystallization. I assume the former since you mention solvent channels. In my experience this is much more likely in the case of soaks, which can often (though not always) be rationalised by the kinetic effect (different rates of exchange of bound and free ligand due to different accessibilities), so the time to attain equilibrium can be much longer than your soaking time, whereas in the case of co-crystallizations it's obviously pre-equilibrated and determined purely by the binding affinity. Even if there are no obvious solvent channels leading from the bulk solvent to the binding sites, a soaked ligand can still get in (particularly if high-affinity which prevents it leaving again), because the protein can "breathe" opening up short-lived channels which close behind the ligand. Cheers -- Ian On Tue, 27 Oct 2020 at 10:29, Christian GALICIA wrote: 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 ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
