COVID-19 data on PDBe-KB pages now focused around specific proteins

PDBe-KB COVID-19 data portal - aggregated views for proteins
16 June 2020

We have now added dedicated pages to the PDBe-KB COVID-19 data portal that display all structural data for specific, mature proteins, therefore making it easier for users to find the exact information they need to support the development of vaccines and therapeutics to compact this pandemic.

 

Like many other viruses, SARS-CoV-2 expresses long  polyproteins, which are subsequently cleaved into functional proteins. The UniProt database contains entries for each polyprotein, while providing annotations highlighting the individual proteins after processing of a given polyprotein.  Previously, we could only display PDBe-KB aggregated views for polyproteins, however we are now able to display all available structural data at the level of the individual proteins.

 

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When you navigate to the PDBe-KB COVID-19 page for the Replicase polyprotein 1ab, it is now possible to view the summary of the available structural data per each processed protein. For the Replicase polyprotein 1ab, there are 190 available structures with 165 different ligands bound. However, these structures are split over multiple proteins, with structures available for 9 of the 15 processed proteins from this polyprotein. Of these, the vast majority of structures are of the 3C-like proteinase, with 142 available structures, containing 130 unique ligands. Beyond this, however, there are 3 more proteins containing at least 10 unique ligands, including the 2'-O-methyltransferase with 18 unique ligands bound.


By viewing these processed protein pages separately, it is much easier to view the key ligand binding sites and potential drug binding regions. For example, in the Ligands and Environments section for the 2'-O-methyltransferase (see image below), the cofactor interaction sites are clearly highlighted, indicating the key amino acids in these interactions.

 

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This is our 4th iteration of the PDBe-KB COVID-19 data portal, and throughout we have been working hard to introduce new features not yet available on our existing PDBe-KB pages. We are now working to incorporate these features, such as these processed proteins pages, download service and antibody annotations, on all PDBe-KB aggregated views for proteins.


If you have any feedback on any of our new features, please let us know at pdbehelp@ebi.ac.uk and help us shape the PDBe-KB resource around you.