The Protein Data Bank (PDB) [1] is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe,[2] PDBj,[3] RCSB,[4] and BMRB[5]). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
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.[6][7]
The file format initially used by the PDB was called the PDB file format. The original format was restricted by the width of For PDB structures determined by X-ray diffraction that have a structure factor file, their electron density map may be viewed. The data of such structures is stored on the "electron density server".[17][18]
Historically, the number of structures in the PDB has grown at an approximately exponential rate, with 100 registered structures in 1982, 1,000 structures in 1993, 10,000 in 1999, and 100,000 in 2014.[19][20] Since 2007, the rate of accumulation of new protein structures appears to have plateaued.[clarification needed]
The file format initially used by the PDB was called the PDB file format. The original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, which is an extension of the CIF format was phased in. mmCIF became the standard format for the PDB archive in 2014.[21] In 2019, the wwPDB announced that depositions for crystallographic methods would only be accepted in mmCIF format.[22]
An XML version of PDB, called PDBML, was described in 2005.[23] The structure files can be downloaded in any of these three formats, though an increasing number of structures do not fit the legacy PDB format. Individual files are easily downloaded into graphics packages from Internet URLs:
http://www.pdb.org/pAn XML version of PDB, called PDBML, was described in 2005.[23]
The structure files can be downloaded in any of these three formats, though an increasing number of structures do not fit the legacy PDB format. Individual files are easily downloaded into graphics packages from Internet URLs:
The "4hhb" is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. (This is not a unique identifier for biomolecules, because several structures for the same molecule—in different environments or conformations—may be contained in PDB with different PDB IDs.)
Viewing the data