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PDB entry overview

The Summary tab gives you a quick snapshot of the key information for a specific PDB entry. Here you’ll find:

  • The source organism of the structure
  • A link to the primary publication
  • A model quality summary
  • An interactive 3D viewer powered by Mol*

Page Layout

At the top of every entry page you’ll see a row of tabs:

  • Model Quality
  • Assembly
  • Macromolecules
  • Ligands and Environment
  • Domains
  • Text annotations
  • Citations

You’ll also find the Download Files menu, which lets you save the structure in several formats.

The Summary Accordion

The collapsible accordion to the right of the graphical viewer in the Summary tab (see below) highlights the most important features of the entry:

  • Preferred assembly (the biologically relevant form of the structure)
  • Number of macromolecules (proteins, nucleic acids, etc.)
  • Domains, ligands, and modifications present in the entry

Expanding each section provides more detail and links the feature directly to the Mol* viewer. For example, clicking on “Ligands” will highlight the ligands in the 3D view. Clicking on one ligand will highlight and then focus the viewer on it. In this way, you can explore the entry in 3D.

PDB entry summary tab PDB entry model quality tab PDB entry macromolecules tab PDB entry ligands and environments tab
Interactive exploration of the nucleosome core particle structure (PDB ID: 4KGC) using the Mol viewer. This composite image demonstrates the functionality of the expandable selection menus for detailed structural analysis. (Top left) The complete nucleosome complex is shown. (Top right) The “Macromolecules” menu is expanded, and Histone H3.2 is selected, highlighting the corresponding in the structural view. (Bottom left) The “Ligands” menu is used to select and zoom in on the ruthenium-containing compound (HRU), shown in a stick representation at its binding site. (Bottom right) The “Domains” menu is expanded to select a specific CATH domain, which is then highlighted in the viewer (orange).

The 3D Viewer and Set Views

In the centre of the page is the Mol* 3D viewer. Here, you can:

  • Switch between pre-set views (e.g. whole assembly, ligand binding site, or specific domain) via the accordion panel
  • Manually explore the structure by zooming, rotating, or changing display styles
  • Using the toggle menu: 
    • Take a snapshot of the current view
    • Expand to full screen for detailed exploration
    • Play animations (e.g. rotating the structure automatically)

For a deeper dive into Mol* functionality, see the Mol* course/tutorial. https://molstar.org/viewer-docs/