Sandbox 34: Difference between revisions

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== Structure ==

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow.<ref name="Structure" /> The single chain is separated into two domains that form a cleft in which the active site resides.<ref name="PDBSum" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The hydrophobic residues are illustrated in grey, and the polar residues are illustrated in magenta. It is easy to see that the <scene name='Sandbox_34/~~Pap_hydrophobic_focus~~/1'>hydrophobic regions</scene> ~~tend towards~~ the interior of the molecule, ~~while the <scene name='Sandbox_34/Pap_polar_focus/1'>~~polar ~~residues</scene> tend~~ towards the exterior of the molecule.

Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow.<ref name="Structure" /> The single chain is separated into two domains that form a cleft in which the active site resides.<ref name="PDBSum" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in grey, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the <scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar regions</scene> segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.

=== Ligands ===

Sandbox 34: Difference between revisions

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 == Structure ==
-Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow.<ref name="Structure" /> The single chain is separated into two domains that form a cleft in which the active site resides.<ref name="PDBSum" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The hydrophobic residues are illustrated in grey, and the polar residues are illustrated in magenta. It is easy to see that the <scene name='Sandbox_34/Pap_hydrophobic_focus/1'>hydrophobic regions</scene> tend towards the interior of the molecule, while the <scene name='Sandbox_34/Pap_polar_focus/1'>polar residues</scene> tend towards the exterior of the molecule.
+Papain is a relatively simple enzyme. It consists of only one chain of 212 residues with three disulfide bonds, illustrated in yellow.<ref name="Structure" /> The single chain is separated into two domains that form a cleft in which the active site resides.<ref name="PDBSum" /> A modified cysteine residue with a sulfhydryl group, <scene name='Sandbox_34/9pap_sulfhydryl_group/1'>cysteine sulfonic acid</scene>, is necessary for the activity of the enzyme.<ref>http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/papain.html</ref> In 9PAP, the sulfhydryl group has been oxidized. Papain contains many <scene name='Sandbox_34/Hydrophobicpolar/1'>hydrophobic and polar regions</scene>. The <scene name='Sandbox_34/Hydrophobic_residues/1'>hydrophobic residues</scene> are illustrated in grey, and the <scene name='Sandbox_34/Polar_residues/1'>polar residues</scene> are illustrated in magenta. It is easy to see that the <scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar regions</scene> segregate themselves such that hydrophobic residues are buried within turns or the interior of the molecule, and that polar regions are towards the exterior of the molecule.
 === Ligands ===