Protein Data Bank in Europe
Knowledge BaseBackground
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
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
Latest release
01 Mar 2023
PDBe-KB update
- User interface improvements
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.