The Protein Data Bank (PDB) is a repository for 3D biological macromolecular structures that includes proteins, nucleic acids, and viruses obtained primarily through X-ray crystallography and NMR spectroscopy. Founded in 1971, it is currently managed by the Research Collaboratory for Structural Bioinformatics and holds over 120,000 released structures. While originally using the PDB file format, newer formats like mmCIF and PDBML aim to make structure files more self-contained.

1. Structure database: PDB
Prepared by
Chandan N Dipke
Assistant Professor
MGM’s College of CS & IT Nanded (MS)
Email: cdipke@gmail.com

2. Protein Data Bank
• A repository for 3-D biological macromolecular structure.
• It includes proteins, nucleic acids and viruses.
• Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%).

3. Protein Data Bank
• Founded in 1971 by Brookhaven National Laboratory, New York.
• Transferred to the Research Collaboratory for Structural Bioinformatics (RCSB)
in 1998.
• Currently it holds 1,20,000 released structures.

4. PDB data formats
• PDB file format was used to contain the coordinates
and related information.
• In the late 1990’s, macromolecular Crystallographic
Information file (mmCIF) evolved.
• mmCIF and PDBML
– Push in to make structure files completely self-contained
descriptions of the experiment and details of the structure
determination.
– PDB file format unstructured and obsolete

5. PDB File Format
• Text file – you can edit with a text editor e.g.
WordPad
• Atomic co-ordinates
• Rich annotation
– Citation
– Experimental Method
– Biological source e.
– Etc.