Sandbox 37: Difference between revisions

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{{Template:Oberholser_Sandbox_Reservation}}
{{Template:Oberholser_Sandbox_Reservation}}
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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Matt's Beautiful Protein' />


='''Papain'''=
The <scene name='Sandbox_37/Matt_adenylate_kinase_37/1'>Adenylate Kinase</scene> protein is shown here with alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange).


==Introduction==
The <scene name='Sandbox_37/Matt_helix_beta_colored/1'>Secondary Structure</scene> of the protein is shown here with alpha helices (green) and beta sheets (blue) highlighted appropriately.
[[Image:Papaya.jpg | right| thumb| ''Carica papaya'']]
<scene name='Sandbox_37/Main_scene/1'>Papain</scene>  


==Structure==
The <scene name='Sandbox_37/Matt_hydrogen_bonds_good/1'>Hydrogen Bonds</scene> of chain A of the protein are highlighted in orange here.
<StructureSection load='9PAP' size='400' align='left' caption='Papain (9PAP)' scene=''></StructureSection>


<scene name='Sandbox_37/Papain_beta-alpha/1'>secondary structure</scene>
The <scene name='Sandbox_37/Matt_hydrophobic_good/1'>Hydrophobic Interactions</scene> are shown here in red.


<scene name='Sandbox_37/Papain_hydrophobic/7'>hydrophobic residues</scene>
The <scene name='Sandbox_37/Matt_hydrophilic_good/1'>Hydrophilic Interactions</scene> are shown here in black.


<scene name='Sandbox_37/Papain_polar/1'>polar residues</scene>
The <scene name='Sandbox_37/Matt_solvent/1'>Solvent</scene> , which is water, is shown here in red. Water's primary location is on the outer parts of the protein, or the hydrophilic regions.


<scene name='Sandbox_37/Ligand/3'>ligands</scene>
The side chains that interact with the <scene name='Sandbox_37/Matt_ligand/1'>ligand</scene> are shown here in crimson. The interactions occur with the hydrophobic side chains. The rest of the protein is faded blue.


<scene name='Sandbox_37/Papain_van_der_waals/1'>van der Waals interactions</scene>
The <scene name='Sandbox_37/Matt_catalytic_residues/1'>catalytic residues</scene> of this protein are shown here in lime green.
 
<scene name='Sandbox_37/Papain_hydrogen_bonds/1'>hydrogen bonds</scene>
 
<scene name='Sandbox_37/Papain_disulfide_bonds/1'>disulfide bonds</scene>
 
==Mechanism==
[[Image:Papain mechanism.jpg | right| thumb| Mechanism of papain catalysis]]
 
<scene name='Sandbox_37/Papain_active_site/1'>active site</scene>
 
==Function==
 
==Inhibition==
<scene name='Sandbox_37/Papain_inhibitor/3'>inhibitor</scene>
 
<scene name='Sandbox_37/Papain_inhibitor_van_der_waals/2'>van der Waals</scene>
 
<scene name='Sandbox_37/Papain_inhibitor_hydrogen_bond/1'>hydrogen bonds</scene>
 
<ref>http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1POP&params.chainEntityStrategyStr=all</ref>
<ref>http://www.worthington-biochem.com/pap/default.html</ref>
<ref>http://en.wikipedia.org/wiki/Papain</ref>
<ref>http://www.pdb.org/pdb/explore.do?structureId=9PAP</ref>
<ref>http://www.britannica.com/EBchecked/topic/441803/papain</ref>
<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref>
 
==References==
<references />
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