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: rrowl...@colgate.edu
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
