Quick Start Guide: Exercise 16


Superimposing Proteins and Fixing Entries

Align related proteins in the Workspace using the Quick Align tool, then compare structures by fixing entries.

Superimposing with Quick Align

The fastest way to superimpose closely related proteins is with the Quick Align tool:
  • Import the PDB structures 4TVG, 4TVH and 4Z4X using File > Get PDB...
  • Include all three entries in the 3D Workspace
  • Click Quick Align on the Favorites toolbar to align the three proteins
  • Optionally add ribbons to the structures to confirm that the alignment was successful
For more control over the protein alignment, use Protein Structure Alignment or Binding Site Alignment, both available from the Task Tool (Tasks > Browse > Structure Alignment).

Comparing structures

To visually compare the structure of 4TVH to the other two crystal structures:
  • Clear the Workspace by choosing Workspace > Clear Entries from the top menu
  • Fix the 4TVH structure in the Workspace by double-clicking the circle next to its name in the Entry List
  • Now click the circle next to 4TVG to include that entry in the Workspace (the 4TVH structure will remain as well), and visually compare the two structures
  • Click the circle next to 4Z4X to include that structure in place of 4TVG, and again compare the structures
  • Exclude the 4TVH structure by right-clicking the entry in the Entry List, then choosing Show in Workspace > Exclude from the menu

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