Introduction

What are Versions?

PDB archives the experimental data and coordinates of all polymeric and small molecules included in a structure. Structures represent a specific chemical and structural state of the biological molecule(s) included in the experiment. Structural coordinates and related chemical information deposited by the authors are the primary data, while metadata such as the protein name, who solved the structure, experimental details, literature information, etc. are secondary data.

The first release of a PDB entry with a specific PDB identifier is called version 1 of the structure.

Any set of changes to metadata is considered a minor revision, and the updated version of the file is assigned a number with an increment of 0.1 to the last version of the entry.

Any change that impacts the chemistry and or coordinates of all or parts of the structure is considered a major revision and the version number is incremented by +1. Learn more about versions of PDB entries.

Why have Versions?

PDB entries (experimental data, coordinates, and metadata) are downloaded and/or linked to by many resources and publications. Changing the PDB ID every time any change or update is made would be confusing for users. For that reason, an updated entry instead retains the same PDB ID with a new version number.

To inform all users that changes have been made to an entry, the updated entry with a new version number is re-released during the next weekly update. This alerts automated scripts and pipelines that an updated version of the file is available. Older major versions are also retained and available for reference. The numbered versioning allows users to track which changes were included in the latest version and why those changes were made. This knowledge can help users make informed decisions about use of an entry.

Documentation

The Structure Summary page provides a short versioning summary. The Versions tab records the complete history with options to download all major versions of the entry.

The Interface

The version history is presented in a tabular format as shown in Figure 1. It includes the version number, versioning date, type and reason for re-releasing (versioning) the entry, changes made and the PDBx/mmCIF categories impacted.

The current version of each entry is available for download from Structure Summary pages. Older versions can be downloaded from the table on the Versions tab.

Figure 1. Tabular representation of the version history of the PDB entry pdb_00006m17 (as of March 2026).

Learning about the Structure

For example, things can be learned about PDB ID pdb_00006m17 from the versions history (see Figure 1) include:

• In versions 1.1 through 1.5 of the structure, minor changes were made in specifying the biological assembly, database references, source of protein, etc. These changes do not impact the chemical and structural information of any part of the structure.
• Version 2.0 involved changes to the coordinates of the structure. These changes were related to the carbohydrate remediation of the archive. Since the proteins in this entry are glycosylated, representation of sugars in the entry was updated to match the current standards.
• Version 3.0 was released with an author-provided coordinate replacement to improve and correct the structure. Following this, the protein name(s) were updated in version 3.1