Protein Data Bank in Europe Knowledge Base
Background
PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is an open, collaborative consortium for integration and enrichment of 3D-structure data and functional annotations to enable basic and translational research. The 3D-Beacons Network , a vital part of the PDBe-KB consortium activities, provides integrated access to experimental and computational protein structure models.
PDBe-KB is a flagship of the ELIXIR 3D-BioInfo Community , an international group of researchers and software developers working on improving use of macromolecular structure data in life science research.
Our mission
- Implement a comprehensive, FAIR infrastructure for macromolecular structures and their annotations
- Enrich macromolecular structure data with strutural and functional annotations to establish their biological context
- Develop innovative tools for data access and visualisation
Key features
Experimental and Predicted Protein Structures
Superposition of Protein Chains and Ligands
Functional and Biophysical Annotations
Case studies
Aminoglycoside phosphotransferase (APH) is an enzyme which is part of a large family of kinases called Macrolide phosphotransferases (MPH). MPHs are found in several pathogens and confer resistance against a large range of macrolide antibiotics. MPHs compromise the binding of a macrolide to a pathogen’s ribosome and inactivate the drug. Using PDBe-KB pages, you can investigate the binding modes of various antibiotics in this enzyme and understand how this enzyme can bind to a wide range of antibiotics. Learn more
Replicase polyprotein 1ab is a multifunctional protein involved in the transcription and replication of viral RNAs. This polyprotein is processed by the SARS-CoV-2 proteases into non-structural proteins, and inturn promote the production of smaller, subgenomic RNAs that encode four main structural proteins and other accessory proteins. Therefore, these proteases play a vital role in the life cycle of coronavirus. Using PDBe-KB pages, you can investigate the structural features of SARS-CoV-2 responsible for its virulence and spot some similarities in the protein structures of SARS-CoV-2 and its close relative SARS-CoV. Learn more
P0DTD1: Macromolecular interaction between papain-like protease nsp3 and ubiquitin-like protein ISG15
License and citation
All of the data provided is freely avaialble for both academic and commercial use under Creative Common Attribution 4.0 (CCBY 4.0 ) licence terms. If you use this resource, please cite the following paper:
PDBe-KB consortium, PDBe-KB: collaboratively defining the biological context of structural data , Nucleic Acids Research, Database Issue (2022)
FAQ
How is PDBe-KB different from PDBe?
PDBe-KB is an open consortium of data providers who derive or assign functional, biophysical or biochemical annotations for macromolecular strutures. PDBe-KB data resource, maintained at EMBL-EBI collates the annotations from PDBe-KB consortium partners and makes these accessible via PDBe-KB portal. PDBe-KB is a sister resource of PDBe , which as a member of the wwPDB consortium , is primarily responsible for archiving experimental macromolecular structure data.
How can I submit annotations to PDBe-KB?
PDBe-KB is an open consortium, and we welcome data providers who would like to make their annotations openly available to the scientific community. Please refer to the “Join PDBe-KB” page for detailed information on why and how to join this collaborative effort.
Can I submit annotations without becoming an official member of PDBe-KB?
While PDBe-KB is an open consortium, all consortium members agree to a collaboration guideline so that we can ensure the quality and governance of the data provided. Consequently, it is not currently possible to make annotations available via PDBe-KB without officially joining the consortium.
Who should I contact with enquiries?
If you would like to get in touch, either to provide suggestions, feedback or to suggest new annotations or wish to become a member of the consortium, you can either visit the Feedback page and fill in a feedback form, or send an email to pdbekb_help@ebi.ac.uk .
How do I download superposed coordinates?
When viewing superposed structures or superposed ligands on the PDBe-KB aggregated views of proteins, you can click on the “Export Models” button on the left-hand side of the screen. This will allow you to download all the currently displayed, superposed structures in mmCIF or binaryCIF formats.