General Information
What's included? Structures in the PDB that contain the words 'Glycosylation Site' in their PDBML file are included in the database
Theoretical Models - the database does not contain theoretical models from the PDB
Point to Note - It should be noted that the information within the database has been obtained from PDBML files. The information has not been validated and inconsistencies in PDBML file sturcture may lead to errors in the data held although many steps have been taken to hopefully avoid this.
Glossary of Terms in Dougal
B factor/occupancy
flag - a flag has been added if the average B-factor for any of the sugar
residues within a glycosylation is above 100 or if the average occupancy value for any of the sugar residues in a
glycosylation is below 1
Resolution - a value of 999 has been assigned to any NMR or Electron Microscopy structures
GlycoID Each glycosylation within a PDB has been assigned a code (GlycoID). It is composed of the name of the type, number and chain of the amino acid to which the glycosylation is attached. For example a glycosylation at Serine 105 in Chain A would have the code SER:105:A
Glycosylation Length - Refers to the number of sugar residues attached to the protein in each glycosylation
Expressed - Refers to whether a protein has been expressed in a non native host cell. Different organsims and tissue types attached different sugars to the same proteins