Protein Data Bank (PDB) is a public collection of three-dimensional structures of macromolecular complexes experimentally determined by X-ray crystallographers and NMR spectroscopists.
There are three ways to search the PDB:
- using the PDB ID codes
- using Search Lite
- using Advanced Search.
PDB ID code is a unique four-character alphanumerical code assigned to every structure in the databank. The characters in the code might be numbers 0-9, and the uppercase letters from A to Z. The PDB ID codes are often reported in the articles as a reference to the structure of a biomolecule.
Search Lite allows you to search databank using the keywords about the biomolecule you are interested in. The examples of search queries are given here.
And Search Fields allows you to create very specific queries.
The data in the Protein Data Bank is stored in the special format, so called PDB format. If you are interested in the format specification, you can click here. This is a format that SPDBV (and other visualization programs) reads. It contains information about position of every atom in a molecule, as well as some auxilary information such as citations and comments.
Example: Structure of Myoglobin (1MBN):
