Bound Structures

The “Bound Structures” tab shows all proteins that interact with the given ligand. The information is presented in two views: Proteins and Structures.

• Protein View groups together all PDB entries associated with the same protein. For each protein, it lists the protein name, EC number (when available), and the functional role of the ligand showing whether the ligand acts as a reactant, cofactor, or drug-like molecule when bound to that protein.
• Structure View expands this information to the level of individual PDB entries. This view provides detailed structure-by-structure data, allowing users to explore each specific complex in which the ligand is observed.

Exercise
1. Determine how many proteins have this ligand bound.
2. Determine how many PDB structures contain this ligand.
3. Locate all PDB structures for Human Tyrosine-protein kinase ABL1. Choose one structure and examine the Imatinib binding site.
(Hint: Check the total number of structures in the Protein view, then switch to Structure view to list each entry. Click the PDB ID and chain to open the Ligands and Environments page on the PDBe entry, where you can explore interacting residues in both 2D and 3D.)
4.Identify the water molecule that clashes with the ligand in this structure.
5. Can you locate this water molecule in the 3D viewer and measure its distance from the ligand?
6. Do any ligand-binding residues show poor fit to the electron density (e.g., RSRZ outliers)?
(Hint: Click on 'Macromolecules' tab of the PDBe entry page and scroll down and compare ‘Chains’ and ‘Ligand binding sites’ track in ProtVista viewer)