Kisker lab: 5B5Q: Difference between revisions
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<scene name='78/781027/Paneld/3'>Panel D:</scene> The active site residues Cys 345, His, and Asp form the catalytic triad. Instead of showing omit density like in the paper, we are showing 2Fo-Fc <jmol><jmollink><text>density</text><script>isosurface s_one color silver "http://proteopedia.org/wiki/images/6/61/Map.jvxl" mesh</script></jmollink></jmol>. Center on <jmol><jmollink><text>His 275</text><script>zoom *3; select 275 and sidechain; center selected; background black</script></jmollink></jmol>. | <scene name='78/781027/Paneld/3'>Panel D:</scene> The active site residues Cys 345, His, and Asp form the catalytic triad. Instead of showing omit density like in the paper, we are showing 2Fo-Fc <jmol><jmollink><text>density</text><script>isosurface s_one color silver "http://proteopedia.org/wiki/images/6/61/Map.jvxl" mesh</script></jmollink></jmol>. Center on <jmol><jmollink><text>His 275</text><script>zoom *3; select 275 and sidechain; center selected; background black</script></jmollink></jmol>. | ||
===Superposition with product complex of SENP8=== | ===Superposition with product complex of SENP8=== | ||
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===Substrate binding site=== | |||
Before you look at the shape of the binding site of Cdu1, you probably will want to show the overall view of again: <scene name='78/781027/Panela/3'>Panel A</scene>. | |||
<scene name='78/781027/Bonus/5'>Bonus figure:</scene> The active-site cysteine sidechain acting as a nucleophile in the hydrolysis reaction is buried surprisingly deeply, barely visible in the surface view (yellow patches on the gray surface). The alpha helix (also shown in yellow) inserted between strand 1 and 2 is above the substrate binding cavity, with Val 271 blocking access to the active site. | |||
</StructureSection> | </StructureSection> | ||