Protein Data Bank or PDB is an online computer-based directory that contains the crystal structure of biological macromolecules such as proteins and nucleic acids along with the supplementary information about the source of the macromolecule and how it was obtained, resolution of the diffraction data and related literature citations.
Protein Data Bank was first established in Brookhaven National Laboratory (BNL) in 1971. It can be accessed worldwide through the internet where users can access the 3D crystal structure of biological macromolecules such as proteins and nucleic acids of any organism. Later Protein Data Bank of the BNL was acquired by the Research Collaboratory for Structural Bioinformatics (RCSB) in 1998.
In the Protein Data Bank, different types of data of the macromolecules such as X-ray crystallography, NMR spectroscopy or cryo-electron microscopy, and related literature of citations can be obtained that were submitted by the biologists and biochemists through the Protein Data Bank deposition centers. After deposition, these data are processed and verified and after then, all these data are available worldwide through the internet.
Process of data deposition and different deposition centers around the world
Research institutions require their researchers to submit any new crystal structure data of proteins or nucleic acids to be submitted to the Protein Data Bank through email or through the wwPDB Deposition tool available at http://deposit.wwpdb.org/deposition/ that upon further processing will be available worldwide. Data submission is necessary which can help other researchers to know about the new advances in the structure that will help them with their research.
Protein Data Bank is now in collaboration with many other institutions around the world for data deposition. However, to maintain uniformity in the final archive of all the data, all protein data deposition centers require the same format and content of the final files and the methods used. Currently, European Bioinformatics Institute is the one that processes the data submitted via AutoDep (http://autodep.ebi.ac.uk) and after processing, EBI sends the data for the central storage at RCSB in the form of PDB format.
RCSB Protein Data Bank
Protein Data Bank here is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB) (http://www.rcsb.org/pdb/home/home.do) where users can perform simple to complex queries on protein and nucleic acid data and they can also analyze these data and visualize the result in different forms. It also acts as the deposition center where users can deposit their crystal structure data that upon processing can be available worldwide to the users free of cost.
World Wide Protein Data Bank
It is an international organization for the Protein Data Bank where you can validate protein data reports and servers. You can also submit your crystal structure data here for the deposition. To visit the World Wide Protein Data Bank visit its website at www.wwpdb.org
European Protein Data Bank
It is another Protein Data deposition center maintained by the European Bioinformatics Institute, a part of the European Molecular Biology Laboratory (embl-ebi). Here crystal structure data can be obtained freely. European bioinformatics institute also provides professional training in bioinformatics and performs basic research. To perform search queries about a protein or gene just put the name of the protein or gene in the search box of the homepage (www.ebi.ac.uk) and hit the search button.
For example, I performed a search query about angiotensin-converting enzyme and I found the following information as seen in the image given at the top. Here you can filter the search results based on your interest. If you want information about enzyme or protein family or macromolecular structure or gene expression data or literature you can select any of these options located on the left side of the search result page.
Protein Data Bank Japan
It is another Protein Data Bank located in Japan (http://pdbj.org/). It is similar to the one maintained by the European Bioinformatics Institute where you can search for any data on the structures related to proteins and nucleic acids. You can also get other related information about the 3D structure such as a source of protein or nucleic acids, methods used to get the 3D structure, related literature cited, etc.
As seen in the picture below, I performed a search query about angiotensin-converting enzyme and I found some information that can be further selected to get more details about the target protein.
