PDBe-KB COVID-19 data portal

PDBe-KB COVID-19 Data Portal

An unprecedented number of scientific efforts are taking place worldwide in order to help combat the new coronavirus epidemic (COVID-19). One of the biggest challenges in this fast-moving situation is to share data and findings in a coordinated way, in order to understand the disease and to develop treatments and vaccines.

To support research efforts to understand more about the SARS-CoV-2 virus and the structures of its proteins, we have created dedicated PDBe-KB pages to highlight important structural features from released PDB entries. These pages include all observed ligand binding sites and protein-protein interaction residues, to help researchers easily identify important structural features to support the development of treatments and vaccines.

The pages available are listed below, with links to the relevant PDBe-KB protein pages:


PDBe-KB page Data Summary

P0DTD1 - Replicase polyprotein 1ab

The orf1ab polyprotein is a multifunctional protein involved in the transcription and replication of viral RNAs. It contains the proteinases responsible for the cleavages of the polyprotein.

P0DTC1 - Tt Replicase polyprotein 1a

The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3.

P0DTC2 - Spike glycoprotein

Spike glycoprotein attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 and CLEC4M/DC-SIGNR receptors and internalization of the virus into the endosomes of the host cell induces conformational changes in the S glycoprotein. Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.

P0DTC9 - Nucleoprotein

Nucleoprotein packages the viral genome RNA into ribonucleocapsid and helps in virion assembly. It also plays important role in viral replication and subgenomic viral RNA transcription.

P0DTC7 - Protein 7a

Protein 7a - Non-structural protein which is dispensable for virus replication in cell culture.


In addition to these pages, EMBL-EBI has set up the COVID-19 Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research.