Protein Data Bank

What kind of data does this resource provide?

The Protein Data Bank (PDB) is a comprehensive resource that contains detailed information about experimentally determined atomic-level, three-dimensional (3D) structures of biological macromolecules, primarily proteins and nucleic acids. Information archived in the PDB and associated EMDB and BMRB data repositories includes 3D atomic coordinates, supporting experimental data, biological assembly information, biopolymer sequences, and related metadata. A paper published in Nucleic Acids Research in 2019 describes the resource in detail.

Give me an example of the impact of this resource.

The PDB accelerates research across the sciences, literally from Agriculture to Zoology, by making complete, rigorously validated, expertly biocurated 3D structure information for biological macromolecules freely available with no limitations on usage under the most permissive Creative Commons CC.0 licence.

The impact of PDB data and structural biologists on United States Food and Drug Administration’s new drug approvals has been documented in both anecdotal and quantitative studies.? An analysis presented in a 2020 cover article published in Drug Discovery Today explained how open access to PDB data facilitated the discovery and development of over 90% of anticancer new molecular entities approved between 2010 and 2018. Additional broad-ranging studies have examined the impact of PDB data on subject areas in fundamental biology, biomedicine, energy sciences, and biotechnology innovation.

PDB data also contributed substantially to the fight against the COVID-19 pandemic. The PDB houses more than 4,600 SARS-CoV-2-related structures (~2% of archive holdings), including more than 1,900 structures of the spike protein.? The role played by PDB structures in Moderna’s mRNA vaccine design was described in a paper published in Nature. Pfizer’s SARS-CoV-2 Main Protease (MPro) inhibitor, nirmatrelvir (the active ingredient of Paxlovid), was the product of a structure-guided drug discovery campaign launched with the aid of the first PDB structures of SARS-CoV MPro (PDB ID 1q2w) and SARS-CoV-2 MPro (PDB ID 6lu7), as described in a paper published in Current Opinion in Structural Biology.

Key Facts

• The PDB was Established in 1971 at Brookhaven National Laboratory (BNL) in Upton, New York, USA.
• Today, the PDB is managed by the Worldwide Protein Data Bank (wwPDB) consortium, an international collaboration encompassing five Core Members: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, based in the US), PDBe (Protein Data Bank in Europe), PDBj (Protein Data Bank Japan), the Biological Magnetic Resonance Data Bank (BMRB, based in the US and Japan), and the Electron Microscopy Data Bank (EMDB, based in the UK), plus an Associate Member: Protein Data Bank China (PDBc: based in the People’s Republic of China).
• The PDB contains more than 225,000 experimentally determined structures of proteins, nucleic acids, and macromolecular machines and their complexes with one another and small-molecule ligands (e.g., enzyme co-factors, approved drugs).
• The majority of atomic-level 3D structures found in the PDB archive were determined by macromolecular crystallography, followed by electron microscopy and nuclear magnetic resonance spectroscopy.
• The PDB provided the trusted data that enabled the transformative advances recognised by the 2024 Nobel Prize in Chemistry to David Baker, Demis Hassabis, and John Jumper.

https://www.wwpdb.org/