Conservation and variation in PDBe-KB protein pages

PDBe-KB news - conservation added to protein pages
07 November 2019

The PDBe-KB aggregated views of proteins ( now have even more information, including sequence conservation, CATHb domains and UniProt variation data, along with faster loading times. 


The most recent release of the protein pages at PDBe-KB includes additional information that provides more comprehensive structural and functional context for your protein of interest. One of the highlights in this new release is the residue-level sequence conservation for each protein, based on 3DPatch, displayed as a graph of conservation levels in the “Functional Annotations” section. Even more detailed information is provided in the fully expanded and zoomed-in view (i.e. until 150 or less residues are shown), with the specific residues and property conservation displayed and highlighted by coloured bars that clearly indicate the conservation for each amino acid.


Sequence conservation component in PDBe-KB protein pages

We are adding more comprehensive residue variation information to the PDBe-KB protein pages, with data from UniProt on known and predicted variants already being displayed. In the near future, this will be complemented with data on prediction of effects of mutations on the conformational stability of the protein from Missense3D and FoldX teams.


Programmatic access to all the data we display on these pages is further improved, with a more responsive and optimised set of REST API endpoints. You can use this service to quickly retrieve large data sets of annotations to support your research:


We would like to thank all the collaborators of PDBe-KB for providing their annotations ( With their help, we are continuing to make protein-centric PDB data richer and more accessible through our PDBe-KB aggregated views. We are grateful for your feedback, so if you have any comments or queries then please provide this via the feedback option on our pages.