Sandbox 35
From Proteopedia
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<scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> | <scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> | ||
| - | <scene name='Sandbox_35/Active_site_papain/ | + | <scene name='Sandbox_35/Active_site_papain/2'>active site</scene> |
| - | + | ===Distribution of Residues=== | |
<scene name='Sandbox_35/Hydrophobic_papain/1'>non-polar and polar residues</scene> | <scene name='Sandbox_35/Hydrophobic_papain/1'>non-polar and polar residues</scene> | ||
| Line 27: | Line 27: | ||
<scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene> | <scene name='Sandbox_35/Nonpolar_papain/2'>non-polar residues</scene> | ||
| + | ===Ligands interactions=== | ||
<scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/2'>Cathepsin L specific inhibitor</scene> | <scene name='Sandbox_35/Cathepsin_l_specific_inhibitor/2'>Cathepsin L specific inhibitor</scene> | ||
Primarily hydrogen bonds with non-water and hydrophobic interactions | Primarily hydrogen bonds with non-water and hydrophobic interactions | ||
Revision as of 01:43, 13 November 2011
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
Papain
Introduction
finds its origin from the latex of the papaya fruit and is classified as a sulfhydryl protease.
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http://www.pdb.org/pdb/explore/explore.do?structureId=2PAD
• Show the secondary structures.
• Compare the distribution of polar residues to that of nonpolar residues.
• Highlight the active site.
• If you can find a PDB file of the enzyme that contains a pseudo-substrate (may be inhibitor), highlight it.
• Show the contacts or attractions that are present between the pseudo-substrate and the protein, and if the enzyme has multiple subunits, show the contacts between the subunits.
• Identify any other ligands that are present in the structure and the types of contacts that are present between them and the protein
http://proteopedia.org/wiki/index.php/Sandbox_55#cite_note-18 Table of contents Pictures References (cross links)
