Protein Data Bank in Europe
Knowledge Base

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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

Compare the superposed structures of protein chains and AlphaFold predictions by clicking on the “3D-view of superposed structures” button on PDBe-KB pages. View example

Superposition of Protein Chains and Ligands

Overlay all the observed bound molecules on representative conformations of a protein segment across the complete PDB archive. View example

Functional and Biophysical Annotations

PDBe-KB partners provide a wide array of functional and biophysical annotations for proteins and small molecules. PDB ProtVista.

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

Q47396: Superposed ligands of aminoglycoside phosphotransferase

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P0DTD1: Macromolecular interaction between papain-like protease nsp3 and ubiquitin-like protein ISG15

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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

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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)

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