Overview: Grouping Structures

Introduction

Biological molecules change their shape and interactions in response to changes in their environment. As these molecules bind to partner proteins, nucleic acids, carbohydrates and various small molecule ligands (e.g., ions, cofactors, inhibitors, drugs) their molecular conformations and interactions change allowing them to perform their specific functions. Each experimental structure in the Protein Data Bank (PDB) or computed structure models (CSMs) that includes all or a specific part of the molecule, provides a glimpse of the molecule in a specific context. To learn about the range of the molecule’s conformations, interactions, and functions it is important to integrate relevant information about the molecule from multiple 3D structures and a variety of data resources to visualize, analyze, and compare the structures of the molecule in a variety of contexts.

Grouping structures with similar amino acid sequences and examining their properties and 3D structural features of these sequence clusters may provide insights about conservation of 3D features to support the molecular mechanisms of specific biological functions. Learn more about sequence clusters and 3D structures.

What is Grouping Structural Data?

Grouping structural data helps gather information about and explore multiple structures at a level higher than an individual structure.

Each 3D structure available from RCSB.org is presented with information and annotations gathered from a variety of public bioinformatics data resources. Learn more about the integrated data and annotations.

Grouping data in RCSB.org helps gather multiple structures related by a specific property (e.g., sequence) or investigational theme. Examining these groups of structures can help identify and explore conservation and/or trends in the properties, features, and functions of molecules in the group.

The grouping data approach described here can help gather 3D structures (experimental structures and CSMs) and organize them by specific molecular properties or investigational themes. Currently the RCSB.org provides options for exploring

• predetermined groups of 3D structures
• based on structure depositor defined criteria - e.g., PDB Deposit Group IDs
• based on molecular properties - e.g., sequence identity, UniProt identifiers
• custom groups of 3D structures
• to organize search results of a query by sequence similarity, UniProt identifiers

How can grouping structures help you?

Grouping structures can provide a broader understanding of the molecule’s structure, function, and evolutionary relationships.

Examples

Explore Grouped data to learn about

• 3D structures of myoglobin grouped by 30% sequence identity and displayed as groups.
• Different protein targets of the drug imatinib - grouped by 30% sequence identity and displayed as groups.
• Representative structures of proteins in the viral polyprotein with UniProtKB Accession P0DTD1 - grouped by 30% sequence identity and displayed as representatives.