Protein Data Bank

Also known as PDB

international open access database of protein and nucleic acid structures

Key facts

Description: Protein structure X-ray crystallography cryoEM NMR Structure Determination
Primary citation: PMID 30357364
Data format: mmCIF , PDB
Website: www .wwpdb .org ebi.ac.uk www .rcsb .org bmrb .io pdbj .org

via Wikipedia infobox

Described at

RCSB PDB: PDB History

The PDB was established in 1971 at Brookhaven National Laboratory under the leadership of Walter Hamilton and originally contained 7 structures.

rcsb.org →

October 2011 Molecule of the Month features historic structures that set the foundation for the PDB archive. In 2003, the Worldwide Protein Data Bank (wwPDB ) was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. It consists of organizations that act as deposition, data processing and distribution centers for PDB data. CARB/NIST left RCSB PDB in 2005 (see Emeritus RCSB PDB Leadership ). In 2021, RCSB PDB and the wwPDB celebrated the 50th Anniversary of the PDB with symposia, materials, and more. Nobel Prize in Chemistry: to David Baker for computational protein design and to Demis Hassabis and John M. Jumper for protein structure prediction Nobel Prize in Chemistry Carolyn Bertozzi, Morten Meldal, K. Barry Sharpless for the development of click chemistry and bioorthogonal chemistry Nobel Prize in Chemistry: Emmanuelle Charpentier and Jennifer A. Doudna for the development of a method for genome editing Nobel Prize awarded to Frances H. Arnold for the Directed Evolution of Enzymes Nobel Prize in Chemistry: Robert J. Lefkowitz and Brian K. Kobilka for studies of G-protein-coupled receptors Nobel Prize in Chemistry: Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for studies of the structure and function of the ribosome Nobel Prize in Chemistry Roger D. Kornberg for his studies of the molecular basis of eukaryotic transcription Carter, A.P., Clemons, W.M., Brodersen, D.E., Morgan-Warren, R.J., Wimberly, B.T. and Ramakrishnan, V. (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature , 407, 340-348. Nobel Prize in Chemistry: Paul D. Boyer and John E. Walker for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine

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Article

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryogenic electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, BMRB and the EMDB).

The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene Ontology.