Protein Data Bank (file format)

pdb

Filename extension	.pdb, .ent, .brk
Internet media type	chemical/x-pdb
Type of format	chemical file format

The Protein Data Bank (pdb) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The pdb format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, observed sidechain rotamers, secondary structure assignments, as well as atomic connectivity. Structures are often deposited with other molecules such as water, ions, nucleic acids, ligands and so on, which can be described in the pdb format as well. The Protein Data Bank also keeps data on biological macromolecules in the newer mmCIF file format.

The PDB file format was invented in 1976 as a human-readable file that would allow researchers to exchange protein coordinates through a database system. Its original format was limited to 80 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates. Through the years the file format has undergone many changes and revisions. As of 13 July 2011^[update], the most recent revision is 3.30.

A typical PDB file describing a protein consists of hundreds to thousands of lines like the following (taken from a file describing the structure of a synthetic collagen-like peptide):

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