PDB File Formats

The primary data format for PDB data is the PDBx/mmCIF format. See a guide to the format and a complete reference of the mmCIF dictionary for more information. PDB data are also offered in XML format (PDBML) following the same PDBx/mmCIF dictionary. In some cases, data are offered in the legacy PDB file format.

PDB entries without legacy PDB-format files

Several types of PDB entries are unable to be represented in the legacy PDB file format

• Entries deposited after July 21, 2027 (announcement)
• Entries containing multiple character chain ids
• Entries containing > 62 chains
• Entries containing > 99999 ATOM coordinates
• Entries that have complex beta sheet topology, see more details
• Entries containing B-factors > 999.99
• Entries that have chemical IDs (for ligands and chemical components) that are 5 characters long. Learn more about chemical IDs.

Note that the entries listed above can be found using Advanced Search (under Deposition > Compatible with PDB Format > equals > N). This is the query.

Historically, large files containing >62 chains and/or 99999 ATOM lines were "split" across multiple PDB format files. These files were combined into single entries at the end of 2014 (wwPDB Announcement).

The wwPDB has extended the PDB ID format to 12 characters. This format includes the prefix ”pdb_” followed by 8 alphanumeric characters, e.g. pdb_1000axyz. In addition to accommodating PDB growth for the foreseeable future, this new ID format enables text mining detection of PDB entries in literature and allows for more informative and transparent delivery of revised data files.

During a transitional phase, PDB entries are assigned both a four-character and its corresponding 12-character ID that places the original 4 characters at the end of the “pdb_0000” prefix:. For example, entry 9o0b is also assigned pdb_00009o0b. Once the wwPDB stops issuing 4-character ID codes (July 21, 2027), new entries will only be issued an extended ID and will be distributed only in PDBx/mmCIF format.