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 < christian.galicia.diaz.sant...@vub.be> 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 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/
