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. Most of the information in that database pertains to proteins, and the pdb format accordingly provides for rich description and annotation of protein properties. However, proteins are often crystallized in association with other molecules or ions such as water, ions, nucleic acids, drug molecules...
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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. Most of the information in that database pertains to proteins, and the pdb format accordingly provides for rich description and annotation of protein properties. However, proteins are often crystallized in association with other molecules or ions such as water, ions, nucleic acids, drug molecules and so on, which therefore can be described in the pdb format as well.
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 :
Through the years the file format has undergone many changes and revisions. Its original format was dictated by the width of computer punch cards (80 columns). The most recent revision is 3.2.
Molecular visualization software capable of displaying pdb files:
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