The fourth character is simply a placeholder that differentiates the ring conformations that are built. There are currently three that are used (4uA1/4uA2/4uA3) that build the 1C4, 2So, and 4C1 conformations (not necessarily in that order). This is currently only performed for IdoA due to the flexibility of the ring compared to other monosaccharides.

Note that tLeap ignores the fourth character when reading PDB files.


On Tue, Dec 19, 2017 at 11:48 AM, Laura Morris <[log in to unmask]> wrote:
Recently I've gotten a PDB file from that contains residues 4uA1 and 0uA1.

Why is there a 1 in the residue designation and are these really 4uA and 0uA?

Laura C. Morris
Scientific Computing Professional
Prestegard & Edison Labs
Complex Carbohydrate Research Center
[log in to unmask]

This email has been checked for viruses by Avast antivirus software.

David F. Thieker, Ph.D.
Biochemistry and Molecular Biology
Complex Carbohydrate Research Center
University of Georgia, Athens, GA