PDBj

PDBj stands for Protein Data Bank in Japan. It is a member of the worldwide Protein Data Bank (wwPDB) consortium that coordinates international repositories of macromolecular structural data. PDBj collects, curates, and distributes 3D structural data of biological macromolecules, including proteins, nucleic acids, and complexes. It provides deposition support and ensures consistency with global data standards.

The database consolidates structures derived from X-ray crystallography, NMR spectroscopy, cryo-electron microscopy, and other methods. Structures receive unique PDB IDs and are integrated with related resources such as sequence databases and taxonomy. PDBj participates in the wwPDB validation and data integrity processes, producing validation reports and updates to reflect community standards.

PDBj maintains an online portal for searching, retrieving, and downloading structure data. It offers deposition services for researchers to submit new or revised structures for addition to the global PDB, along with guidance on metadata and validation. It also provides programmatic access via APIs or bulk download options, enabling computational analyses and integration into third-party pipelines.

As one of the wwPDB partner centers, PDBj helps ensure global uniformity of data formats (such as PDB and mmCIF) and interoperability across regional databases. It serves the Japanese scientific community and international users by providing multilingual support and educational resources about structural biology and data standards.