The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the internet. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as theNIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.
The PDB database is updated weekly (on Tuesday). Likewise, the PDB Holdings List is also updated weekly. As of 21 September 2010, the breakdown of current holdings was as follows:
| Experimental Method | Proteins | Nucleic Acids | Protein/Nucleic Acid complexes | Other | Total |
| X-ray diffraction | 55480 | 1231 | 2605 | 17 | 59333 |
| NMR | 7512 | 925 | 162 | 7 | 8606 |
| Electron misroscopy | 214 | 17 | 77 | 0 | 308 |
| Hybrid | 24 | 1 | 1 | 1 | 27 |
| Other | 126 | 4 | 4 | 13 | 147 |
| Total: | 63356 | 2178 | 2849 | 38 | 68421 |
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