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Yikes! This cuts close to my area. We occasionally have undergrads solve and refine carbonic anhydrase-sulfonamide structures as a part of a 4-hour biochemistry teaching lab. (We have a whole shelf-full of sulfonamides that make excellent teaching projects.) _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [log in to unmask] On 10/17/2013 12:55 PM, Ethan A Merritt wrote: > On Thursday, 17 October, 2013 10:51:08 Lucas wrote: >> Dear all, >> >> I've been lecturing in a structural bioinformatics course where graduate >> students (always consisting of people without crystallography background to >> that point) are expected to understand the basics on how x-ray structures >> are obtained, so that they know what they are using in their bioinformatics >> projects. Practices include letting them manually build a segment from an >> excellent map and also using Coot to check problems in not so good >> structures. >> >> I wonder if there's a list of problematic structures somewhere that I could >> use for that practice? > 4KAP is a nice cautionary example of failing to properly refine a ligand > after placement. > > - Open coot, download 4KAP + map from EDS. > - Navigate to ligand and view difference density map. > - Oops. > - Now open up residue information for the ligand. Notice anything odd? > > For bonus points, look up the known ligation chemistry of this site. > Notice that the binding pose of the 4KAP ligand does not match it. > > Ethan > >> Apart from a few ones I'm aware of because of (bad) >> publicity, what I usually do is an advanced search on PDB for entries with >> poor resolution and bound ligands, then checking then manually, hopefully >> finding some examples of creative map interpretation. But it would be nice >> to have specific examples for each thing that can go wrong in a PDB >> construction. >> >> Best regards, >> Lucas