Does anyone out there have some insight into, or a credible explanation
for, why PDB ligand id XYP (beta-D-xylopyranose) has what seems like
non-standard atom notation, at least compared to other sugars!
The standard atom naming convention for nearly all monosaccharides,
including XYS (alpha-D-xylopyranose), is to name the ring carbons C1, C2
etc and their attached oxygens O1, O2 etc - perfectly logical and
understandable.
However, XYP has a totally different naming scheme. This makes
automatically defining sugar linkages (based on atom naming) very difficult.
Quite apart from not understanding the logic of the naming convention
for XYP, even more confusingly, XYP replaced the now deprecated 3-letter
code for beta-D-xylopyranose (HSZ), and this older version has the more
standard notation.
Thanks
Andrew
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*Dr. Andrew J. Sharff D.Phil**
*Research Scientist / Software Developer
Global Phasing Ltd
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UK
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