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The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, is released into the public domain, and can be accessed for free. The database is the central repository for biological structural data.

1 Contents

As of 1 October, 2004, the database contained 27,428 released atomic coordinate entries (or "structures") and took in about 2,000-3,000 new ones per year. Data is stored in the mmCIF format specifically developed for the purpose. Note that the database stores information about the exact location of all atoms in a large biomolecule; if one is only interested in sequence data, i.e. the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used.

Through the years the PDB has undergone many, many changes and revisions. Its original format was dictated by the width of computer punch cards.

RCSB PDB Guide The PDB format specification can be found here, and it is vital that you read this before looking at the raw data.
ftp.rcsb.org The raw data can be downloaded from here.
www.rcsb.org Statistics about the PDB can be found here.

This legacy format has caused many problems with the format, and consequently the PDB has three distinct 'clean-up' projects;

The Molecular Modeling DataBase (MMDB) from NCBI
The Macromolecular Structure Database from the European Bioinformatics Institute
The Data Uniformity Project from PDB

Each of these grant-funded projects has attempted to achieve the same goal via different routes. The Data Uniformity Project is hosted by the RCSB (the current home of the PDB). Each uses the original PDB data to derive a new format; The MMDB uses ASN.1 (and an XML conversion of this format); The MSD uses a Relational Database; The Data Uniformity Project uses mmCIF (and another XML conversion of this format).

Some people would say that this is a Good Thing; others would argue that, without a universal repository of information (i.e., a common dictionary), how can we talk about the same thing.

Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.

If a biologist submits structure data for a protein or nucleic acid, PDB staff reviews and annotates it. The data is then automatically checked for plausibility. The source codeSource code (commonly just source or code is any series of statements written in some human-readable computer programming language. In modern programming languages, the source code which constitutes a software program is usually in several text files, but for this validation software has been released for free. The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure predictionProtein structure prediction is one of the most significant tasks tackled in computational structural biology. It has the aim of determining the three-dimensional structure of proteins from their amino acid sequences. In more formal terms, this is the pre).

Various funding agencies and scientific journals now require scientists to submit their structure data to PDB.

2 History

Founded in 19711971 is a common year starting on Friday (click for link to calendar). Events January January 1 British divorce Reform Act comes into force January 2 66 die in stairway crush at Rangers v Celtic football match, Glasgow, Scotland. See Ibrox disaster. Janua by Brookhaven National LaboratoryBrookhaven National Laboratory is a national laboratory located in Upton, New York on Long Island, and was formally established in 1947 at the site of a former U. Brookhaven is operated for the United States Department of Energy by Brookhaven Science Asso, the Protein Data Bank was transferred in 19981998 was a common year starting on Thursday (see link for calendar), and was designated the International Year of the Ocean''. Events January January 1998 A massive ice storm, caused by El Nino, strikes New England, southern Ontario and Quebec, resulting to the Research Collaboratory for Structural Bioinformatics (RCSB), which is composed of Rutgers UniversityRutgers, The State University of New Jersey is located in New Brunswick, Piscataway, Camden and Newark, New Jersey. Considered a highly prestigious university, Rutgers offers more than 100 distinct bachelor's, 100 master's, and 80 doctoral and professiona, the University of Wisconsin, Madison, NIST and the San Diego Supercomputer Center. Funding comes from the National Science Foundation, Department of Energy, National Library of Medicine and the National Institute of General Medical Sciences. The European Bioinformatics Institute in the UK and the Institute for Protein Research in Japan also collect, process and submit data files.

The PDB is a key resource in structural biology and is critical to more recent work in structural genomics.

Countless derived databases and projects have been developed to integrate and classify the PDB interms of protein structure, protein function and protein evolution .

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Topics: Protein Data Bank Pdb Format Database Structural Structure...

Proteinmyoglobin, showing coloured alpha helices. This protein was the first to have its structure solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, which led to them receiving a Nobel Prize in Chemistry. A protein is a complex,	Protein biosynthesisnucleus of the cell light blue , genes (DNA, dark blue are transcribed into RNA. This RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA red that is then transported out of the nucleus and into the cytoplasm p	Protein kinaseA protein kinase is an enzyme that can transfer a phosphate group from a donor molecule (usually ATP) to an amino acid residue of a protein. The protein kinase mechanism is used in signal transduction for the regulation of enzymes: phosphorylation can act
Protein phosphataseProtein phosphatases are enzymes that remove phosphate groups that have been attached to amino acid residues of proteins by protein kinases. The phosphates are important in signal transduction by regulating the proteins they are attached to. To reverse th	Protein targetingProtein targeting includes the mechanisms by which a biological cell transports proteins to the appropriate organelle for insertion into a membrane or secretion to the outside. This article deals with protein targeting in eukaryotes except as noted. Prote	ProteinoidProteinoids are protein-like molecules formed inorganically from amino acids. Some theories of abiogenesis propose that proteinoids were a precursor to the first living cells. The inorganic polymerization of amino acids into proteins through the formation
Protein folding	Protein Data Bank	Proteinuria
Protein catabolism	Protein engineering	Protein sequencer
Protein (band)	Protein structure prediction	Protein subunit

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