Sandbox Reserved 660: Difference between revisions
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==AMP-binding pocket== | ==AMP-binding pocket== | ||
[[Image:The image of interaction.png | thumb]] | |||
The AMP binding pocket is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the binding site ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333. | The AMP binding pocket is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the binding site ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333. | ||
