New branched polysaccharide representation for polymeric carbohydrates in the PDB

Carbohydrate molecules now have a new representation in the PDB
29 July 2020

The representation of polymeric carbohydrates in the PDB has been updated, including information about linkages between sugars and with standardised nomenclature, while the PDBe website now includes improved visualisation of these molecules and their interactions.

 

A new representation of polymeric carbohydrates has been introduced in the PDB, to improve the findability and representation of these molecules. This new representation describes all the observed components from the polysaccharide and includes information about their linkages, along with standard nomenclature and annotated glycosylation sites. For information about the changes in the PDB archive, see the news item on the wwPDB website.

 

To support this new carbohydrates representation, we have introduced some changes to our PDBe pages to allow clear identification of these molecules on both entry pages and search results. On PDBe entry pages for structures containing branched carbohydrates, these molecules are clearly highlighted in the Ligands and Environments section, including the individual monosaccharides and their stoichiometry in these structures. This section links to specific carbohydrate polymer pages that give more information about these molecules, along with interactive components displaying the environments in 2D and 3D.

 

LigEnv and Mol* components displaying carbohydrate interaction data

The LigEnv (left) and Mol* (right) components, as displayed for a carbohydrate polymer in PDB entry 1zag. These components are interactive, with highlighting of specific components in the LigEnv viewer also highlighted in the Mol* as shown in this case with BMA F 3.

 

The carbohydrate polymer pages give the standard nomenclature for the carbohydrate molecule, indicating the individual components of the molecule and specific linkage types. The main features of this page are the LigEnv and Mol* components, displaying the carbohydrate interactions in an interactive environment. The new LigEnv component displays all the individual components of the carbohydrate polymer, indicating their linkages with bold, solid lines. In addition, it also highlights any interactions that the individual carbohydrates monomers make with other parts of the structure, including other covalent linkages, polar contacts and weak interactions. These interactions are calculated using Arpeggio software, with the whole list of interaction types described in the Arpeggio publication. To ensure correct interpretation of atomic interactions, the ‘addh’ command in ChimeraX is used to add hydrogens to the structure, which are not modelled in most PDB entries.

 

Furthermore, upon clicking on an individual carbohydrate monomer in the LigEnv component, this view is expanded to indicate the specific atomic interactions for this monosaccharide. This includes interactions between the adjacent monomers in the carbohydrate polymers and also with other residues and ligands in the structure. This highlights specific details about the types of interactions and the distance between the atoms.

 

LigEnv and Mol* showing specific atomic interactions between ligand and environment

The LigEnv (left) and Mol* (right) components, as displayed for a carbohydrate polymer in PDB entry 1zag. BMA F 3 has been selected in the LigEnv viewer, expanding it to highlight the specific atomic interactions for this component, while it is also highlighted in green in Mol*.

 

The LigEnv component has been introduced across all the Ligands and Environments pages at PDBe, allowing users to easily view all the interactions between a ligand and its environment in a PDB entry.


If you have any feedback regarding these changes then please contact us at pdbehelp@ebi.ac.uk. Any feedback related to a specific PDB entry, then please use the ‘feedback’ button on the PDBe page.