About the PDB Archive and the RCSB PDB

The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

The PDB archive is available at no cost to users. The PDB archive is updated each week at the target time of Wednesday 00:00 UTC (Coordinated Universal Time). The most recent release is timestamped and linked on every page in the top right header.

The PDB was established in 1971 at Brookhaven National Laboratory and originally contained 7 structures. In 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) became responsible for the management of the PDB. In 2003, the wwPDB was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. It consists of organizations that act as deposition, data processing and distribution centers for PDB data.

In addition, the RCSB PDB supports a website where visitors can perform simple and complex queries on the data, analyze, and visualize the results. Details about the history, function, progress, and future goals of the RCSB PDB can be found in our Annual Reports and Newsletters.

The PDB Advisory Notice defines the conditions for using data from the PDB archive.

RCSB PDB staff are located at Rutgers, The State University of New Jersey and the University of California, San Diego. Watch this video for a tour of the Rutgers site;

• http://www.youtube.com/watch?v=akmXIy7XQwA

Some of the protein from the RCSB Protein Data Bank (PDB)

• Amylase

Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.

• Trysin

The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors.

• Pepsin

X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution.

• HtrA

Solution structure of HtrA PDZ domain from Streptococcus pneumoniae and its interaction with YYF-COOH containing peptides.

• Carboxypeptidase

Insight into the stereochemistry in the inhibition of carboxypeptidase A with N-(hydroxyaminocarbonyl)phenylalanine: binding modes of an enantiomeric pair of the inhibitor to carboxypeptidase A.

The RCSB Protein Data Bank: site functionality and bioinformatics use cases

Annotation	Ontology/Database	Description
Biological process	GO Consortium	Controlled vocabulary that describes biological processes
Cellular component	GO Consortium	Controlled vocabulary that describes the cellular location
Molecular function	GO Consortium	Controlled vocabulary that describes the molecular function
Enzyme classification	Enzyme Commission (EC) system recommended by the IUBMB	Classification system for the reactions catalyzed by enzymes
Transporter classification	Transporter Classification (TC) system recommended by the IUBMB	Classification system for membrane transport proteins that  incorporates both  functional and phylogenetic information
Medical subject terms	MeSH terms developed by the National Library of Medicine	Controlled vocabulary to describe medical terms;  used for indexing of PubMed abstracts
Source organism	NCBI taxonomy	A curated set of names and classifications of  organisms from superkingdoms to subspecies
Genome location	Entrez Gene	Location of genes in the genomes of various organisms for  proteins in the PDB.  The top level in the hierarchy is the organism's genome.  Each genome expands into chromosomes,  which in turn expand into a list of loci on  the chromosomes.
Fold/domain classification	SCOP	Hierarchical structural classification of proteins that  provides a  description of structural and evolutionary relationships  of proteins of known structure
Fold/domain classification	CATH	Hierarchical structural classification of protein domains.  Each protein has  been divided into structural domains and assigned  into homologous superfamilies.