Protein Data Bank

What is Protein Data Bank?

• A repository for 3-D biological macromolecular structure.
• It is obtained by using crystallography or NMR spectroscopy.
• Founded in 1971 by Brookhaven National Laboratory, New York
  -PDB is an important resource for research in the academic, pharmaceutical, and biotechnology sectors
  
  
• Format is save in mmCIF(macromolecular Crystallograhic Information File)

• The dictionary definition language (DDL)  is structured in a way that data files that conform to this syntax can be readily loaded into a database

Software tools...

• pdb-extract
• ADIT
• PDB Validation Suite

Data Query....

Compound Information	Myoglobin,Lysozyme
Number of chains	1-5
Secondary structure content	Present of alpha min 80%

• Example of protein data bank content.

NAME	EXPLANATION
Structure of ClpP in complex with ADEP1	Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. The structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2.

 

NAME	EXPLANATION
TRYPSIN INHIBITOR (T1) FROM NICOTIANA ALATA	The three-dimensional structures of a series of 6-kDa trypsin inhibitors isolated from the stigma of the ornamental tobacco Nicotiana alata have been determined by 1H NMR spectroscopy combined with simulated annealing calculations