3D Structure of Human Urokinase and Known Inhibitor
3D Structure of Human Urokinase and Known Inhibitor
This is human urokinase and you are seeing it displayed in "cartoon" form and colorized to help you see the secondary structure of this protein.
Reset and the structure.
Zoom in and look at one of the tubes created by b sheets.
Is this tube filled with side chains or does it remain essentially a passageway?
The backbone has retained its coloring but now the side chains have been added and they are colored so that each amino acid is a different color.
What amino acids fill the tube? You can find out by clicking on each one and reading the display in the lower left corner of the browser window.
Is the other tube similar or does it look different?
You are looking at the other tube without any side chains displayed.
What do you think about the symetry of this protien? Zooming out will help you evaluate it better.
Now let's find out where the inhibitor binds. We will need to zoom out and display the inhibitor.
This is a familiar view for the protein but now we can see the inhibitor too, just above the open tube.
Zoom in and look at the inhibitor more closely.
This is
not
the same inhibitor Vicki Nienaber and her collaborators discovered by her novel approach of incubating the crytalized protein in a solution containing many different compounds.
Click here
to see a diagram of the inhibitor that was isolated by incubating the crystalized urokinase with a mixture of comounds.
What does this inhibitor look like when displayed with its Van der Waal radii displayed?
Notice how nicely it fits into a fold of the protein.
What similarities are there between this inhibitor and the one Nienaber discovered? What are the differences?