Protein Feature View

The Protein Feature Viewer provides graphical summaries of PDB protein biological and structural features and their relationships with UniProtKB entries. Protein alignments and features are loaded from RCSB PDB web services including the main data API and the 1D Coordinate Server. These resources integrate information from multiple resources and databases. Structural features such as secondary structure, angle/distance outliers, protein-ligand binding sites or disulfide bridges, are extracted from the PDB structural data. Additionally, structural domains are annotated from CATH and SCOPe databases. Biochemical and biomedical features are collected from the UniProtKB database and mapped onto PDB sequences.

Responsive and Interactive Properties

  • Zoom using the mouse scroll (wheel) or the mousepad/touchpad to see more details and to show the sequence amino acids
  • To zoom using the mousepad/touchpad hover over the Protein Feature View, and move/drag 2 fingers in an up and down motion
  • Once zoomed, left click and drag to move the panel left or right (using either a mouse or touchpad)
  • Left click on a feature to highlight the annotated region or right click to select and highlight a custom area
  • Hovering over track features will display a legend at the top right corner of the viewer (see Feature Tooltips)


  • The first track defines the sequence reference over which features are mapped
  • A white circle over the start (or end) of a block indicates that the feature in its original reference does not start (or end) in that position but before (or after)
  • A dashed line between blocks indicates that in the original reference the feature is connected and therefore a sequence insertion has occurred
  • Color flags (blue/orange) between track titles and track features indicates feature provenance (blue for RCSB PDB and orange for third party resources)

Structure Summary Page - Sequence Tab

In the Sequence Tab (e.g. 4hhb) the Protein Feature Viewer will display the full range of available features (structural and biological annotations) and the alignments between Polymer Instances (chains) and UniProtKB sequences. The select menu can be used to display the features for the different PDB Polymer Instances (chains) of the current Entry.

Structure Summary Page - Main Tab

The Protein Feature Viewer in the Structure Summary Pages (e.g. 4hhb) displays the alignments between PDB Entity sequences and UniProtKB. Additionally, it includes Entity features such as mutations and artifacts, and the different regions that has not been (or partially) observed at Instance level. The select menu can be used to change the reference (Entity/UniProtKB) over which features are mapped and displayed.

Feature Tooltips

Feature tooltips contain important information about feature positions in the current and original reference sequence. Tooltips are displayed when mouse hovering features on the top right corner of the Protein Feature Viewer

  • (i) Feature short name description
  • (ii) Database source or software name used to obtain the feature. Color indicates its provenance (blue RCSB PDB and orange third party resources)
  • (iii) Feature position in the current reference system
  • (iv) PDB residue author Ids associated to the feature position
  • (v) Feature source database/software name
  • (vi) Feature original reference entry Id and positions
  • (vii) Feature description

For Developers

The Protein Feature Viewer is an Open Source project written in TypeScript. It is available at

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Last updated: 2/3/2021