Sandbox Reserved 1852: Difference between revisions
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==General Structure== | ==General Structure== | ||
[[Image:Squidbpropeller2.png|230px|left|thumb|Figure. 1 Beta-propeller Scaffold]] | |||
====Scaffold==== | ====Scaffold==== | ||
After early Rosetta computational modelling, an ideal protein scaffold was found in the 6-bladed [https://en.wikipedia.org/wiki/Beta-propeller beta-propeller] of ''Loligo vulgalis,'' or the Europoean Squid. <ref name="Siegel"/><ref name="Scharff">PMID:11435114</ref> The protein is relatively simple, with only one chain, one unit, 324 residues, and no extra ligands, metal ions, or small molecules bound. | After early Rosetta computational modelling, an ideal protein scaffold was found in the 6-bladed [https://en.wikipedia.org/wiki/Beta-propeller beta-propeller] of ''Loligo vulgalis,'' or the Europoean Squid. <ref name="Siegel"/><ref name="Scharff">PMID:11435114</ref> The protein is relatively simple, with only one chain, one unit, 324 residues, and no extra ligands, metal ions, or small molecules bound. | ||
[[Image:BindingPocket.png|300px|right|thumb|Figure | |||
[[Image:BindingPocket.png|300px|right|thumb|Figure 2. Active Site]] | |||
====Active Site==== | ====Active Site==== | ||
In the active state, there are <scene name='10/1075254/Active_site/3'>two catalytic residues</scene> that aim to stabilize the transition state of the Diels-Alder reaction. The Y134 acts as a <scene name='10/1075253/Y134_h_donation/1'>hydrogen bond donor</scene> to the oxygen on the <scene name='10/1075253/Ligand/6'>ligand</scene>. Q208 acts as a <scene name='10/1075253/208_bond_donor/1'>hydrogen bond acceptor</scene> to the nitrogen on the ligand. These interactions help reduce the energetic gap between orbitals allowing the reaction to proceed, outlined in HOMO/LUMO. | In the active state, there are <scene name='10/1075254/Active_site/3'>two catalytic residues</scene> that aim to stabilize the transition state of the Diels-Alder reaction. The Y134 acts as a <scene name='10/1075253/Y134_h_donation/1'>hydrogen bond donor</scene> to the oxygen on the <scene name='10/1075253/Ligand/6'>ligand</scene>. Q208 acts as a <scene name='10/1075253/208_bond_donor/1'>hydrogen bond acceptor</scene> to the nitrogen on the ligand. These interactions help reduce the energetic gap between orbitals allowing the reaction to proceed, outlined in HOMO/LUMO. | ||
