Papain: Difference between revisions
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Stefin B consists of five beta sheets wrapped around a five-stranded beta sheet wrapped around a single alpha helix. In Stefin B, the Gly-9 residue along with <scene name='Papain/Stefin_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of Papain. This wedge makes extensive and tight interactions with Papain which involves the embedding of 16% of Stefin B into Papain with a total of 128 intermolecular atom-atom interactions occurring. <scene name='Papain/Stefin_b/3'>Residue segments</scene> Met-6 - Pro-11, Gln-53 - Asn-59, Gln-101 - His-104, Tyr-124 and Phe-125 on the wedge all have some interaction with the enzyme, though Cys-25 is the only one to form a direct contact. All residues from the base of Stefin B, shown in ball-and-stick form, and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene>, shown in gray, are involved in the complex with the inhibitor. | Stefin B consists of five beta sheets wrapped around a five-stranded beta sheet wrapped around a single alpha helix. In Stefin B, the Gly-9 residue along with <scene name='Papain/Stefin_b_hairpin_loops/1'>two hairpin loops</scene>, illustrated in magenta, form a "wedge" complementary to the active site groove of Papain. This wedge makes extensive and tight interactions with Papain which involves the embedding of 16% of Stefin B into Papain with a total of 128 intermolecular atom-atom interactions occurring. <scene name='Papain/Stefin_b/3'>Residue segments</scene> Met-6 - Pro-11, Gln-53 - Asn-59, Gln-101 - His-104, Tyr-124 and Phe-125 on the wedge all have some interaction with the enzyme, though Cys-25 is the only one to form a direct contact. All residues from the base of Stefin B, shown in ball-and-stick form, and both sides of the <scene name='Papain/Stefin_b_active_site_interacti/1'>active site cleft</scene>, shown in gray, are involved in the complex with the inhibitor. | ||
There are a small number of <scene name='Papain/Stefin_b_hbonds/2'>direct hydrogen bonds</scene> (labeled in <scene name='Papain/Stefin_b_hbonds/1'>this scene</scene>, between Stefin B and Papain, however there are many more polar interactions mediated by <scene name='Papain/ | There are a small number of <scene name='Papain/Stefin_b_hbonds/2'>direct hydrogen bonds</scene> (labeled in <scene name='Papain/Stefin_b_hbonds/1'>this scene</scene>, between Stefin B and Papain, however there are many more polar interactions mediated by <scene name='Papain/Stfn_b_solvent_intrxns/1'>solvent bridges</scene>, the solvent being mainly <big><b><font color='darkturquoise'>water</font></b></big>. Thirteen solvent molecules of water bridge polar residues of the enzyme and inhibitor. Seventeen hydrogen bonds are made with a solvent molecule and Stefin B. Fourteen of these bridges form a Papain contact. The rest of the interactions are largely hydrophobic-- involving apolar <scene name='Papain/Stefin_b_vdw/2'>Van der Waals forces</scene>.<ref> PMID:2347312 </ref> | ||
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