Hi Andrew, I can only make a guess: As the atom that actually should be "O1" is called "O4A", and all the other atom names look fine apart from a "B" added to the them, it looks as if this residue was derived from a disaccharide, where the XYP part was linked to O4 of another residue. But I agree with you that the names used in this entry are non-standard.
By the way, HSZ is even worse because there the atoms are numbered the wrong way round, i.e. what should be the C1 is called C5 and vice versa. It would be even more difficult to create a correct sugar linkage based on those atom names. Cheers, Thomas > 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
