Sandbox 34: Difference between revisions
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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 <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>, R in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/1'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" /> Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between | 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 <scene name='Sandbox_34/Subunitsrandl/1'>two domains</scene>, R in purple, and L in gray, that form a cleft in which the <scene name='Sandbox_34/2subuwithactivesite/1'>active site</scene>, consisting of cysteine-25, histidine-159, and asparagine-175, resides.<ref name="PDBSum" /> Many hydrogen bonds exist throughout the molecule, holding it in its 3D conformation. These stabilizing bonds, represented in white, are present both in the <scene name='Sandbox_34/Pap_with_h-bonding_btwnbckbne/1'>backbone</scene>, and between | ||
<scene name='Sandbox_34/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>. 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 primary representation of papain used in this article, 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 gray, 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/Pap_with_h-bonding_btwnsdchns/2'>residues</scene>. Additionally, the molecule is stabilized by nine hydrogen bonds, and three ionic interactions. The strongest | ||
<scene name='Sandbox_34/Arg191asp140intraxn/1'>salt bridge</scene> exists between asparagine-140 and arginine-191. 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 primary representation of papain used in this article, 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 gray, 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 residues</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. | <scene name='Sandbox_34/Hydrophobicpolar/2'>hydrophobic and polar residues</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 === | === Ligands === | ||
