Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community.

Learn more about PDB HISTORY and FUTURE.


Vision and Mission

Vision

Sustain a freely accessible, single global archive of experimentally determined structure data for biological macromolecules as an enduring public good.

Mission

  • Ensure open access to public domain experimentally determined structural biology data.
  • Provide expert deposition, validation, and biocuration services at no charge to Data Depositors.
  • Enable universal access for expert and non-expert Data Consumers with no limitations on usage.
  • Manage the PDB archive as a public good according to the FAIR Principles.
  • Lead the world in structural biology data representation, exchange, and visualization.
wwPDB Members

Collects NMR data from any experiment and captures assigned chemical shifts, coupling constants, and peak lists for a variety of macromolecules; contains derived annotations such as hydrogen exchange rates, pKa values, and relaxation parameters.

Simple and advanced searching for macromolecules and ligands, tabular reports, specialized visualization tools, sequence-structure comparisons, RCSB PDB Mobile, Molecule of the Month and other educational resources at PDB-101, and more.

Rich information about all PDB entries, multiple search and browse facilities, advanced services including PDBePISA, PDBeFold and PDBeMotif, advanced visualisation and validation of NMR and EM structures, tools for bioinformaticians.

Supports browsing in multiple languages such as Japanese, Chinese, and Korean; SeSAW identifies functionally or evolutionarily conserved motifs by locating and annotating sequence and structural similarities, tools for bioinformaticians, and more.

News & Announcements

04/10/2018

Depositors can help the structure modeling community test prediction methods by marking depositions as a CASP target in OneDep. A wide range of targets are needed, with particular interest in membrane proteins, protein complexes, and cryo-EM structures. CASP will also include modeling efforts assisted by sparse experimental data, in collaboration with experimental groups in NMR, SAXS, SANS, crosslinking, and FRET.

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03/27/2018

Validation reports for all PDB structures have been updated to include new percentile statistics reflecting the state of the archive on December 31st 2017 and updated versions of third-party software: CCP4/Refmac (7.0 v44), Phenix (1.13) and Mogul (2018) and CSD archive (as539be). The LLDF statistic previously used to identify ligands that do not fit electron density well has been replaced by a combination of Real-space R-factor (RSR>0.4) and Real-space correlation coefficient (RSCC<0.8). The identification of standard amino acid or nucleotide residues that do not fit the electron density well has been corrected to take into account how reliably Refmac software reproduces the R-factors reported by authors. Documentation at wwpdb.org/validation has been updated to reflect these changes.

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