1pe6: Difference between revisions

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<StructureSection load='1pe6' size='340' side='right'caption='[[1pe6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='1pe6' size='340' side='right'caption='[[1pe6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1pe6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carpa Carpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PE6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1pe6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PE6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Papain Papain], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pe6 OCA], [https://pdbe.org/1pe6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pe6 RCSB], [https://www.ebi.ac.uk/pdbsum/1pe6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pe6 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pe6 OCA], [https://pdbe.org/1pe6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pe6 RCSB], [https://www.ebi.ac.uk/pdbsum/1pe6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pe6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PAPA1_CARPA PAPA1_CARPA]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pe6 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pe6 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
E-64-c, a synthetic cysteine protease inhibitor designed from E-64, binds to papain through a thioether covalent bond. The x-ray diffraction data for 2.1-A resolution were used to determine the three-dimensional structure of this complex and refined it to R = 0.159. 0.159. In the complex structure, the configurational conversion from S to R took place on the epoxy carbon of E-64-c, implying that the nucleophilic attack of the Cys-25 thiol group occurs at the opposite side of the epoxy oxygen atom. The leucyl and isoamylamide groups of E-64-c were strongly fixed to papain S subsites by specific interactions, including hydrogen bonding to the Gly-66 residue. The carboxyl-terminal anion of E-64-c formed an electrostatic interaction with the protonated His-159 imidazole ring (O-...HN+ = 3.76 A) and consequently prevented the participation of this residue in the hydrolytic charge-relay system. No significant distortion caused by the binding of E-64-c was shown in the secondary structure of papain. It is important to note that inhibitor and substrate have opposite binding modes for the peptide groups. The possible relationship between the binding mode and inhibitory activity is discussed on the basis of the crystal structure of this complex.
Refined x-ray structure of papain.E-64-c complex at 2.1-A resolution.,Yamamoto D, Matsumoto K, Ohishi H, Ishida T, Inoue M, Kitamura K, Mizuno H J Biol Chem. 1991 Aug 5;266(22):14771-7. PMID:1860874<ref>PMID:1860874</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pe6" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Papain|Papain]]
*[[Papain|Papain]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Carpa]]
[[Category: Carica papaya]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Papain]]
[[Category: Inoue M]]
[[Category: Inoue, M]]
[[Category: Ishida T]]
[[Category: Ishida, T]]
[[Category: Kitamura K]]
[[Category: Kitamura, K]]
[[Category: Matsumoto K]]
[[Category: Matsumoto, K]]
[[Category: Mizuno H]]
[[Category: Mizuno, H]]
[[Category: Ohishi H]]
[[Category: Ohishi, H]]
[[Category: Yamamoto D]]
[[Category: Yamamoto, D]]
Retrieved from "https://proteopedia.org/1pe6"