PDB mmCIF Entry Index

The Protein Data Bank is the single global archive of experimentally-determined 3D structures of biological macromolecules, established in 1971 and now holding well over 230,000 entries. It stores atomic coordinates for proteins, nucleic acids, and their complexes determined by X-ray crystallography, cryo-EM, NMR, micro-electron diffraction, and integrative methods, along with the underlying experimental data (structure factors, EM maps, NMR restraints) and rich metadata covering sequence, ligands, modifications, oligomeric state, and validation reports. Every entry has a four-character PDB ID (e.g. 7PZB) and is distributed primarily in the mmCIF format, with legacy PDB-format files retained for compatibility.Operationally, the archive is jointly managed by the wwPDB consortium: RCSB PDB at Rutgers and UCSD handles deposits from the Americas and Oceania and serves as the wwPDB Archive Keeper, PDBe at EMBL-EBI handles Europe and Africa, PDBj at Osaka University handles Asia, and BMRB hosts NMR-specific data. All wwPDB sites receive synchronized weekly updates and serve the archive free of charge under CC0. Within structural biology and protein ML, the PDB is the canonical training and validation source for structure prediction (AlphaFold2/3, RoseTTAFold, Protenix, OpenFold), inverse folding (ProteinMPNN, ESM-IF), docking, MD setup, and template-based modelling, and time-cutoff splits on PDB release dates are the standard way to control for data leakage when benchmarking these models.

Splits

The split is deterministic: sha256(pdb_id) % 10 == 0 goes to test; buckets 1 through 9 go to train.

Dataset Statistics

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