Structure of human ubiquitin C-terminal hydrolase 3 (UCH-L3) covalently bound to ubiquitin vinylmethylester (shown in pink). The architecture of this enzyme around the catalytic site closely resembles that of other proteases of the papain clan. The catalytic site consists of a triad of residues in a charge relay system*, from Asp184 to His169 to Cys95.
Unlike proteases from the C19 family, the catalytic site remains properly aligned in the absence of ubiquitin. Instead, the specificity of the interaction of proteases from the C12 family and ubiquitin seems to rely on a loop that occluds the active site in the unliganded enzyme. Upon binding to ubiquitin, a structural rearrangement takes this loop away and exposes the catalytic site.

*See family C26 for a more detailed explanation of the charge relay system in a catalytic triad.



  • Structures are rendered as ribbons. Catalytic and catalytic metal-complexing residues are shown as neons. Inhibitors are displayed as space filling spheres.

  • Carbons are shown in light gray, hydrogens in cyan, oxygens in red, nitrogens in blue, and sulfurs in yellow.

  • Left-click and drag to rotate the protease. Right-click and drag up/down to zoom in/out. Click with both buttons and drag to move the protease. Use the upper bar to get different views and for display options. For a close-up of the catalytic site, choose the cat_site view.

  • Once you have clicked inside the structure window, you can use the keyboard to hide/show objects:

    '1' toggles the ribbon.
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    '3' toggles the catalytic residues.

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  • To hide/show elements in the structure, first you have to click inside the render window.