Exploring a 3D Structure
What are the Structure Summary and related pages?
Each 3D structure accessible from RCSB.org [including experimental or Protein Data Bank (PDB) structures and Computed Structure Models (CSMs)] has a variety of data associated with it.
- Primary data include information about the specific 3D structure - e.g., structural coordinates, sequences of biological macromolecules, information about any small molecules/ligands present in the structure, details about structure determination method(s), authors and publication information.
- Secondary data include
- Information related to one or more components integrated from other data resources, mapped onto the 3D structure(s), and made available at RCSB.org - e.g., functional and mutational information about macromolecule(s) from UniProt.
- Organization and classification of one or more components included in the PDB entry - e.g., sequence and structural domains from Pfam, SCOP, CATH, and ECOD; molecular functions, cellular location, biological functions from Gene Product Annotations; and membrane annotations.
For each experimental structure, the primary and secondary data are presented in a manner that can be easily accessed, visualized, downloaded, and analyzed. This presentation also allows you to use pieces of information to visualize it, integrate information from other bioinformatics resources, and/or query the entire archive for other examples like it.
For each CSM, the primary and a limited amount of secondary data are presented for easy access, visualization and analysis.
This document describes how different types of information about an entry are presented on the Structure Summary and related pages. It also describes how you can use this information to learn more about the properties, interactions, and functions of the specific molecule(s) being studied.
How to access the Structure Summary and related pages?
- If you know the specific identifier for the 3D structure you wish to explore (e.g., PDB ID for experimental structures and AlphaFold or Model Archive IDs for CSMs), you can access the Structure Summary and related pages for the entry by typing the identifier into the top search bar on the RCSB.org home page.
- If you do not have a specific 3D structure of interest, you can Search or Browse the archive based on various parameters to identify one or more structures that you may wish to explore. Click on the ID of any 3D structure of interest listed in the search results to open the Structure Summary and related pages including Structure Summary, 3D View, Annotations, Experiment, Sequence, Genome, Ligands, and Versions.