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 |
