Sent from my LG phone Kendall Nettles <knett...@scripps.edu> wrote:
>Sometimes you can distinguish disorder from the other possibilities if you >have enough structures with the same protein. We have several examples where >part of the ligand is not visible in the maps, but there is clear distortion >of the ligand binding pocket to accommodate the missing piece. for example, we >have one with a ligand that has an extended linker. You can see a big whole in >the protein where the linker leaves the pocket, but no density for the tether. >Kendall >On Apr 11, 2012, at 8:09 AM, Fischmann, Thierry wrote: > >Dipankar, > >Herman's message describes the most common case, by far. In addition to his >excellent post there are 4 other possibilities which I can think of of why, in >general, the e- density may be missing for part of a ligand: >- the compound solution are never 100% pure. One impurity may be the compound >you're trying to soak but missing a specific moiety. This would be a result of >the chemical synthesis: one of the steps would be incomplete and the impurity >was not separated at a later stage. The impurity is what you'll see in the >electron density if it happens to bind significantly more tightly than the >intact ligand. Sometimes this possibility can be excluded just from the >chemical synthesis (unless the purity of some of the starting reagents is >questionable). Or you can check the inhibitor structure by Mass spec. >- compound is not stable in the soak conditions. For instance it may not be >stable at, say, in water, or in acidic conditions, or exposed to visible >light, etc. >- cleavage by the protein: on occasion the protein may be able to cleave the >ligand. This is usually observed if the ligand is a substrate (say 3rd >phosphoryl missing in a soak with ATP) or a close relative of the true >substrate. >- cleavage by X-ray: the compound gets degraded during data collection, fast >enough that a significant part of the data set is collected with the compound >with the missing piece. > >Thierry > >________________________________ >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> >Sent: Wednesday, April 11, 2012 5:39 AM >To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> >Subject: Re: [ccp4bb] Ligand fitting into density > >Dear Dipankar, > >I have had a case where I had soaked the same compound in Trypsin (2.2 Å) and >in Factor Xa (2.0 Å). In Trypsin, one six-membered ring was completely >invisible, despite good resolution and phases, whereas this ring was clearly >visible in the Factor Xa structure. The electron density is shown in >J.Med.Chem (2002)45:2749 figures 1A and 1E. > >It does happen that parts of a soaked compound are completely without electron >density. In these cases I assume that this part is disordered and I refine the >compound without the undefined parts, while in contrast to flexible surface >residues, people look closely at bound compounds and use the structures e.g. >to optimize scoring functions for docking programs. Leaving the undefined >parts in the model in a guessed conformation would likely cause people to draw >wrong conclusions. > >For the rest, if the inhibitor is well-defined in the electron density maps, I >would not worry about the high B factors. They may even normalize once you >leave out the undefined part. > >Best regards, >Herman > >________________________________ >From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dipankar >Manna >Sent: Wednesday, April 11, 2012 11:11 AM >To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> >Subject: [ccp4bb] Ligand fitting into density > >Dear Crystallographers, > >The protein I am working with is having SG P3121, Structure is solved at 2.5A. >the protein was soaked with compound, compound density is also looking >prominent except one six membered ring. There is no density at all for the >particular ring, but other parts of the compound is fitting well enough into >the density. The B factor of the ligand is showing >100. How can I justify >this issue. Asking for suggestions. > >Regards, > >Dipankar Manna > > >________________________________ > >This e-mail and any files transmitted with it are for the sole use of the >intended recipient(s) and may contain confidential and privileged >information.If you are not the intended recipient, please contact the sender >by reply e-mail and destroy all copies of the original message.Any >unauthorized review, use, disclosure, dissemination, forwarding,printing or >copying of this email or any action taken in reliance on this e-mail is >strictly prohibited and may be unlawful. > >Visit us at http://www.aurigene.com >Notice: This e-mail message, together with any attachments, contains >information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, >New Jersey, USA 08889), and/or its affiliates Direct contact information >for affiliates is available at >http://www.merck.com/contact/contacts.html) that may be confidential, >proprietary copyrighted and/or legally privileged. 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