Complexes

The Complexes tab provides detailed information about the quaternary structures (complexes) that can be generated from a PDB entry. Each entry may contain one or more complexes, which describe how individual macromolecular chains (proteins, RNA, or DNA) assemble into a functional unit.

Preferred and alternative complexes

• The left-hand panel lists all possible complexes for the entry (See Figure 1).
• The preferred complex, as defined by PDBe, is the one that contains all unique chains in the smallest possible stoichiometry.
• This definition does not always match the biologically functional complex.
• The right-hand 3D viewer allows interactive exploration of each selected complex.

Example:

• Chaperonin GroEL (PDB ID: 1grl): the preferred complex (Complex 2) is the heptameric ring, as it represents the smallest stoichiometry containing all unique chains.

However, the biologically functional form is the tetradecamer (Complex 1), made up of two stacked heptameric rings.

Why are there multiple complexes?

• For many X-ray crystallography entries, the deposited coordinates describe only the asymmetric unit of the crystal.
• Applying crystallographic symmetry operations can generate different possible complexes.
• Some of these represent the biologically relevant form, while others reflect crystal packing arrangements.

Information provided in the tab

For each complex, the tab lists:

• Name and multimeric state.
• PDBe Complex ID – a stable identifier for each unique complex composition across the PDB archive.
• Predicted properties from PISA (Proteins, Interfaces, Structures and Assemblies), including:
  • Accessible and buried surface area.
  • Dissociation energy and entropy.
  • Number of interfaces.

These values are computational predictions, not experimental measurements. They provide an indication of the likely stability and intermolecular interactions within the complex.

Navigation and links

• Clicking “View more” → jumps to the relevant section of the aggregated Complex page for the selected complex (e.g., summary, structures, ligands, sub/supercomplexes).
• Clicking the PDBe Complex ID → opens a search page listing all PDB entries containing the same complex composition (See below).

Complex pages

Complex pages bring together all the key information about each unique macromolecular complex in the Protein Data Bank (PDB). Each page gives you an overview of complexes, including:

• What the complex is – with a description of its composition, global symmetry, oligomeric state and stable PDBe Complex ID.
• Where it’s found – a list of equivalent PDB assemblies that represent the complex of interest, across the PDB archive.
• Energetics and stability – visualisation and comparison of predicted PISA assembly properties across all instances of this complex.
• What it binds – catalogues of unique small molecules associated with this complex with functional categories (e.g., drug-like, reactant-like or cofactor-like).
• Hierarchical relationships – showing smaller subcomplexes and larger supercomplexes related to the complex of interest.

These pages provide an integrated view of each complex, including its composition, predicted stability, bound small molecules, and its place in the hierarchy of related complexes.

Example: Check out the tetradecamer form of Chaperonin GroEL complex page at https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/complexes/1kp8