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"Group" summary pages and search results simplify exploration of PDB structures with similar sequence identity/UniProt ID or were deposited as part of the same study.
The PDB archive contains many entries that are very similar:
Structures: Some structures were deposited to the PDB together at the same time using the RCSB PDB Group Deposition server. These collections of structures (e.g., structures with same protein/s, but different bound ligands) are assigned a Group Deposition ID that identifies the collection.
Polymer Entities: Multiple PDB entries will contain polymer entities that share similar sequence identity (from 100% to 30%) as well as entities with the same UniProt Accession ID.
New features can be used to explore these "groups":
Grouped search results will highlight the number of structures in a group along with related information (example). Access detailed documentation about this new feature for grouping redundant search results.
Group Summary Pages
UniProtKB Entries with Known 3D Structure
Advanced Search return option can be used to detect similarity among search results and return data in "grouped" sets.
Group Summary Pages provide overviews of key features, properties, sequence alignments, and annotations of any predetermined or custom group.
Mol* (molstar) is a modern, web-based open-source toolkit for visualization and analysis of large-scale molecular data. Mol* is used throughout RCSB.org, from generating the 2D images available for every structure and entity in the PDB; to offering interactive 3D views of structures, sequence annotations on structures, electron density; and close-up views of ligand interactions.
A standalone version of Mol* is also available that allows users to upload custom files and/or superimpose different structures in the same viewer.
To learn more about Mol* at RCSB.org:
For an overview of Mol* features, see "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures" Nucleic Acids Research (2021) 49: W431–W437 doi:10.1093/nar/gkab314.
Additional details about Mol* usage and development are available at Molstar.org.
With each weekly update, the PDB Data Distribution by Experimental Method and Molecular Type table is updated. Each number links to the corresponding set of structures.
These statistics are part of a large collection of PDB Statistics that offer interactive displays of data based upon different criteria. All statistics are generated using Web Services and represent the current holdings of the archive.
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