More download options and antibody annotations on the PDBe-KB COVID-19 pages

PDBe-KB COVID-19 pages
06 May 2020

We recently announced the new PDBe-KB COVID-19 data portal, allowing users to easily access a wealth of structural data from the SARS-CoV-2 virus. We have now added annotations on antibody classifications and details of peptide inhibitor molecules to the interactions section. In addition, we have also extended the bulk download options to entries with specific ligands or macromolecular interactions.

 

The interactions section of the PDBe-KB protein aggregated views previously only identified macromolecules based on Uniprot accession. We have now extended this for the COVID-19 pages to include antibody chains so that these interactions are highlighted. For example, on the PDBe-KB page for the COVID-19 Spike glycoprotein we have included interactions from both the heavy and light immunoglobulin chains (see below image). In addition, we have also added interactions information for peptidic molecules in the Biologically Interesting Molecule Reference Dictionary (BIRD) - these molecules are often inhibitors or other important molecules that are not defined as ‘ligands’ and it is now much easier to view all their interactions with the protein of interest. For example, in the interactions section of the COVID-19 Replicase polyprotein 1ab page, you can view all interactions for a peptide inhibitor found in PDB entry 6lu7.

 

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We recently introduced a new bulk file download service to the PDBe-KB COVID-19 pages, and have now extended this to include download for subsets of entries containing macromolecular complexes or entries with similar structures. In the summary section at the top of the page, you can now download the subset of entries containing ligands, or similar proteins. In addition, in the ligands and interactions sections, you can download a subset of entries containing a specific ligand or entries containing interaction with a particular macromolecule. For example, on the PDBe-KB page for the COVID-19 Replicase polyprotein 1ab, in the Ligands section, you can download only the files that contain S-Adenosylmethionine (SAM) [see below image].

 

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We are continuing to develop the PDBe-KB COVID-19 data portal to ensure that the most relevant data on SARS-CoV-2 protein structures can be made easily available to researchers at this time. If you have any comments or suggestions on these pages, then please contact us on pdbehelp@ebi.ac.uk.