Protein Data Bank

Protein Data Bank

The Protein Data Bank is the picture of the 3-D structural data of the large biological molecules, such as protein and nucleic acid. It describe proteins and other biological molecules by using method such as X-ray crystallography, NMR Spectroscopy and cryo-electron microscopy. The data is submitted for the use of the scientist and it is  accessible by the internet around the world.

The PDB currently contain 29956 structures. Structures deposited by the Protein Data Bank at the Research Collaboratory for Structural Bioinformatics (RCSB) are written in standard format. There are also short description used written in standard format. The data contained in the archive include atomic coordinates, bibliographic citations, primary and secondary structure, information, and crystallographic structure factors and NMR experimental data.

Structures are available for many of the proteins and nucleic acids involved in the central processes of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets, and even whole viruses. However, it can be a challenge to find the information that you need, since the PDB archives so many different structures. You will often find multiple structures for a given molecule, or partial structures, or structures that have been modified or inactivated from their native form.

The examples of protein data bank that we can obtain are:

Structure of subtilisin

Structure of Lon A

Structure of dipeptidase

Struture of carboxypeptidase

Structure of DegP

These images can be obtained by first downloading the files from RCSB Protein Data Bank. All information about the protein are also available. The downloaded files can be opened with RasWin program (RasWin is only for windows users) to view the image of the protein structure. In addition, the downloaded files can be saved as BMP, GIF, EPSF, PPM or RAST by exporting the files to any intended format.

Protein	Main Function
Subtilisin	Protein digesting enzyme
Lon A	Degradation of denatured polypeptides
Dipeptidase	Enzymes secreted by enterocytes into small intestine
Carboxypeptidase	Hydrolize a peptide bond of carboxyterminal
DegP Peptidase	Chaperone in the bacterial envelope