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Sandbox 35

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<scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref>
<scene name='Sandbox_35/2nd_struc_papain_helix/2'>alpha helix</scene> <ref name="9PAP PDB">[http://www.pdb.org/pdb/explore/explore.do?structureId=9PAP]9PAP PDB</ref>
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<scene name='Sandbox_35/Active_site_papain/3'>active site</scene> <ref group="xtra">PMID:8140097</ref>
+
<scene name='Sandbox_35/Active_site_papain/3'>active site</scene> <ref>PMID: 8140097</ref>
 +
 
===Distribution of Residues===
===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>
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==Catalytic Mechanism==
==Catalytic Mechanism==
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[[Image:Papainmech6.jpg|200px|left|thumb| General mechanism of papain catalysis<ref>[http://chemistry.umeche.maine.edu/CHY431/Peptidase10.html] University of Maine</ref>.]]
==References==
==References==
<references />
<references />
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<ref group="xtra">PMID:8140097</ref><references group="xtra"/>
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http://www.pdb.org/pdb/explore/explore.do?structureId=2PAD
http://www.pdb.org/pdb/explore/explore.do?structureId=2PAD
• Show the secondary structures.
• Show the secondary structures.

Revision as of 03:16, 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.


Contents

Papain

Introduction

finds its origin from the latex of the papaya fruit and is classified as a sulfhydryl protease.

Structure of Papain (PDB entry 9PAP)

Drag the structure with the mouse to rotate

Catalytic Mechanism

General mechanism of papain catalysis.
General mechanism of papain catalysis[3].

References

  1. ↑ [1]9PAP PDB
  2. ↑ Wang J, Xiang YF, Lim C. The double catalytic triad, Cys25-His159-Asp158 and Cys25-His159-Asn175, in papain catalysis: role of Asp158 and Asn175. Protein Eng. 1994 Jan;7(1):75-82. PMID:8140097
  3. ↑ [2] University of Maine
  • Wang J, Xiang YF, Lim C. The double catalytic triad, Cys25-His159-Asp158 and Cys25-His159-Asn175, in papain catalysis: role of Asp158 and Asn175. Protein Eng. 1994 Jan;7(1):75-82. PMID:8140097

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)

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