A viewer that visualizes the interactions of bound ligands in protein and nucleic acids structures.
Ligand Explorer has options to turn on the display of interactions including hydrogen bonds, hydrophobic
contacts, water mediated hydrogen bonds, and metal interactions.
A link to Ligand Explorer is available in the Ligand Chemical Component widget on the structure summary page.
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To quickly get information on structural details you may mouse over structural features in the molecular viewer window as well as the sequence viewer at the top.
Information regarding structural details such as residue number and element type is displayed in the status bar at the bottom of the viewer.
carbon - green
hydrogen - white
oxygen - red
nitrogen - blue
sulfur - yellow
phosphorus - orange
First, select a ligand from the left hand menu. If you launched Ligand Explorer from the Ligand Chemical Component widget, a ligand is already selected.
Second, click the check boxes next to the list of interactions to turn on the interactions.
Interacting residues and the distance of the interactions are automatically displayed, as shown in the example below.
Interacting residues are also highlighted with grey boxes in the sequence display.
Each interaction type has a default distance threshold, i.e. 3.3 A for hydrogen bonds. You can change these values by typing in a new value and hitting the Enter key.
Follow the tutorial (click here) for saving high-resolution images.
You can load another structure directly using the file menu using one of three options:
Use the File -> Open PDB ID option to load a new structure by the 4-letter PDB ID (example 1STP).
Use the File -> Open File option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats:
Use the File -> Open ULR option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats:
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.