Sandbox 30: Difference between revisions

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===Residue Distribution===

As can be seen from its <scene name='Sandbox_30/Papain_polarity_ballandstick/3'>ball and stick model</scene>, papain contains a variety of acidic (red), basic (blue), hydrophilic uncharged (pink), and hydrophobic (gray) residues. Since the enzyme operates in free solution, it would be expected that the hydrophilic residues would reside mostly on it exterior, shielding a hydrophobic core. This can be plainly seen from papain's <scene name='Sandbox_30/Papain_polarity_spacefill/3'>space filling model</scene>, in which hydrophilic residues are purple and hydrophobic residues are grey. Upon removal of the hydrophilic residues, the <scene name='Sandbox_30/Papain_hydrophobic_spacefill/2'>hydrophobic core</scene> of the enzyme is easy to see. As with all proteins, it is this hydrophobic segregation that allows the protein to properly fold and maintain a meaningful shape.

===Ligands===

The crystallization procedure used to create the 9PAP structure was carried out using 62% (w/w) methanol and water. Thus, this crystal structure of papain is coordinated by methanol molecules, 29 of which are shown~~. The enzyme is also coordinated by~~ water molecules ~~(not shown)~~, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />.

The crystallization procedure used to create the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium. Thus, this crystal structure of papain is coordinated by methanol molecules, 29 of which are shown, and water molecules, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />. The both methanol and water molecules form a hydrogen bonds with many different parts of the enzyme, while the methanol molecules also interact hydrophobically with it.

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@@ Line 17: / Line 17: @@
 ===Residue Distribution===
 As can be seen from its <scene name='Sandbox_30/Papain_polarity_ballandstick/3'>ball and stick model</scene>, papain contains a variety of acidic (red), basic (blue), hydrophilic uncharged (pink), and hydrophobic (gray) residues.  Since the enzyme operates in free solution, it would be expected that the hydrophilic residues would reside mostly on it exterior, shielding a hydrophobic core.  This can be plainly seen from papain's <scene name='Sandbox_30/Papain_polarity_spacefill/3'>space filling model</scene>, in which hydrophilic residues are purple and hydrophobic residues are grey.  Upon removal of the hydrophilic residues, the <scene name='Sandbox_30/Papain_hydrophobic_spacefill/2'>hydrophobic core</scene> of the enzyme is easy to see.  As with all proteins, it is this hydrophobic segregation that allows the protein to properly fold and maintain a meaningful shape.
 ===Ligands===
-The crystallization procedure used to create the 9PAP structure was carried out using 62% (w/w) methanol and water.  Thus, this crystal structure of papain is coordinated by methanol molecules, 29 of which are shown.  The enzyme is also coordinated by water molecules (not shown), 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />.
+The crystallization procedure used to create the 9PAP structure was carried out using a 62% (w/w) methanol and water crystallization medium.  Thus, this crystal structure of papain is coordinated by methanol molecules, 29 of which are shown, and water molecules, 21 of which occur between adjacent papain molecules and probably important in maintaining their structural integrity<ref name="9PAP PDB" />.  The both methanol and water molecules form a hydrogen bonds with many different parts of the enzyme, while the methanol molecules also interact hydrophobically with it.