Sites

Ligand interactions

This video demonstrates how to visualize receptor-ligand interactions in a PDB file by providing a PDB code, or by uploading your own file.

  • The interactions are listed in table format, and it is possible to filter and order interactions by the values in each column.
  • An interactive 3D viewer showing only the ligand and interacting residues from the receptor is available.
  • Snake and Helix box plots highlighting the interacting residues in red can be downloaded.

Question

  • Look up the recptor ligand interactions in PDB structure 3RZE? How many interactions are found?

Site search - from PDB complex

This video demonstrates how to create a binding site definition by providing a PDB code, or by uploading your own file. The resulting site definition can be used to search for receptors with a similar binding site.

  • A binding site definition can be extracted from a provided PDB code, or an uploaded PDB file.
  • First select the set of receptors that should be compared the the site definition.
  • Once the PDB file has been processed, the site definition can be reviewed and modified.
  • Note the “Min. match” field, which determines how many interactions must match for a receptor to be considered a match.
  • The results page shows a list of matching receptors, followed by a list of non-matching receptors.

Question

  • Create a site definition using PDB structure 3RZE? How many interactions are found?