User:David Canner/Sandbox good
From Proteopedia
(Difference between revisions)
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<center><scene name='HMG-CoA_Reductase/1dq8_starting_scene/1'>Initial Scene (Reset)</scene> </center> | <center><scene name='HMG-CoA_Reductase/1dq8_starting_scene/1'>Initial Scene (Reset)</scene> </center> | ||
The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/2'> The “cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/2'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. It is this K691 that likely stabilizes the negatively charged oxygen of the first mevaldyl-CoA intermediate. The mevaldyl CoA intermediate is subsequently converted to Mavaldehyde with added stabilization from <scene name='HMG-CoA_Reductase/1dqa_h866/2'>H866, which is within hydrogen bonding distance of the thiol group</scene>. It is then believed that the close proximity of <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.<br /> | The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/2'> The “cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/2'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. It is this K691 that likely stabilizes the negatively charged oxygen of the first mevaldyl-CoA intermediate. The mevaldyl CoA intermediate is subsequently converted to Mavaldehyde with added stabilization from <scene name='HMG-CoA_Reductase/1dqa_h866/2'>H866, which is within hydrogen bonding distance of the thiol group</scene>. It is then believed that the close proximity of <scene name='HMG-CoA_Reductase/1dqa_e_and_d/2'>E559 and D767</scene> increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.<br /> | ||
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The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/3'> The“cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/3'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/3'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. Etc… | The HMG binding pocket is the site of catalysis in HMGR. <scene name='HMG-CoA_Reductase/1dqa_cis_loop2/3'> The“cis-loop” that bends over the top of HMG </scene> is a critical structural element of this binding site. Residues <scene name='HMG-CoA_Reductase/1dqa_e_and_d/3'>E559 and D767</scene> and are positioned in the active site as is <scene name='HMG-CoA_Reductase/1dqa_k691/3'>K691 which is only 2.7 angstroms from the HMG O2 carbonyl oxygen</scene>. Etc… | ||
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=====Example from the page [[The Structure of PI3K]] ===== | =====Example from the page [[The Structure of PI3K]] ===== | ||
<center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center> | <center><scene name='User:David_Canner/Sandbox_P/Full/4'>Initial Scene (Reset)</scene> </center> | ||
| - | Compared with: | + | =====Compared with:===== |
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====Tip #3: When Transitioning focus to a new domain, it is best to zoom out and orient the reader to the new domain of interest==== | ====Tip #3: When Transitioning focus to a new domain, it is best to zoom out and orient the reader to the new domain of interest==== | ||
=====Example from the page [[The Structure of PI3K]]:===== | =====Example from the page [[The Structure of PI3K]]:===== | ||
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<scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>The alpha-A helix of NSH2 </scene> (residues 340-345) is anchored into <scene name='User:David_Canner/Sandbox_P/Nsh2_pocket/2'> a cavity created by the C2 and Kinase domain interface.</scene> Helix α11K of the <scene name='User:David_Canner/Sandbox_P/Kinase_domain_out/2'>Kinase domain</scene> (residues 1017-1024) <scene name='User:David_Canner/Sandbox_P/Nsh2_kianse/1'>interacts with the alpha-A helix of nSH2.</scene> nSH2 interacts with the <scene name='User:David_Canner/Sandbox_P/C2_out/3'>C2 domain</scene> through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong <scene name='User:David_Canner/Sandbox_P/Nsh2_charge_charge/3'>salt bridge between NSH2 Glu 349 and C2 residue Arg 357, and hydrogen bonds between NSH2 Glu 348 and C2 Glu 453 and Asp 454.</scene> <ref name="Amzel"/> | <scene name='User:David_Canner/Sandbox_P/Nsh2_full/1'>The alpha-A helix of NSH2 </scene> (residues 340-345) is anchored into <scene name='User:David_Canner/Sandbox_P/Nsh2_pocket/2'> a cavity created by the C2 and Kinase domain interface.</scene> Helix α11K of the <scene name='User:David_Canner/Sandbox_P/Kinase_domain_out/2'>Kinase domain</scene> (residues 1017-1024) <scene name='User:David_Canner/Sandbox_P/Nsh2_kianse/1'>interacts with the alpha-A helix of nSH2.</scene> nSH2 interacts with the <scene name='User:David_Canner/Sandbox_P/C2_out/3'>C2 domain</scene> through a network of charge-charge interactions involving two loops on nSH2 (Residues 374-377 & 350-354) and C2 residues 364-371, a strong <scene name='User:David_Canner/Sandbox_P/Nsh2_charge_charge/3'>salt bridge between NSH2 Glu 349 and C2 residue Arg 357, and hydrogen bonds between NSH2 Glu 348 and C2 Glu 453 and Asp 454.</scene> <ref name="Amzel"/> | ||
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====Tip #4: ==== | ====Tip #4: ==== | ||
=====Example from the page ===== | =====Example from the page ===== | ||
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__NOEDITSECTION__ | __NOEDITSECTION__ | ||
Revision as of 09:29, 21 November 2010
How to Make Excellent Scenes
This is a list of tips and tricks to develop effective scenes for your pages. The scenes below were taken from other pages with effective scenes.
Scene Transitions
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