Ann Taylor Sandbox 118
From Proteopedia
Thrombin
Thrombin is a "trypsin-like" serine protease. Its structure (PDB code 1ppb) is shown here with a peptide chloroketone inhibitor (PPACK). The thrombin A chain (cleaved N terminal fragement) is shown in cyan and the B chain is shown in red. The is made up of a catalytic triad of Ser195, His57 and Asp102, backed up by Ser214. The peptide chloroketone inhibitor (PPACK) is shown in purple. A closeup shows the at which the sidechain of Asp194 makes a salt link with the N-terminus at residue 16, newly formed when the A chain is cleaved in the zymogen-to-enzyme activation process. The specificity pocket is on one side of the throat of the domain 2 beta barrel, and the activation site is close next to it.
The B chain consists of . As is true for all of the "trypsin-like" serine proteases, each of the two thrombin domains consists mainly of a 6-stranded, antiparallel beta barrel. The specificity pocket (here filled with the Lys sidechain of the PPACK inhibitor) is in one side of the throat of the domain 2beta barrel, and the activation site is close next to it.
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Gilman suc-AAPK-trypssin
suc-AAPK-trypssin is a serine protease in the acyl enzyme state. Structure 118 is the form of the acyl enzyme in which tetrahedral intermediate has collapsed and after the first peptide bond has been cleaved. Only one half of the enzyme remains in the active site.
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