1ppp - Revision history

OCA at 05:57, 17 April 2024

OCA — Wed, 17 Apr 2024 05:57:56 GMT

←Older revision		Revision as of 05:57, 17 April 2024
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	<StructureSection load='1ppp' size='340' side='right'caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ppp' size='340' side='right'caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppp]] 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=1PPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppp]] 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=1PPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPP 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]] 1.9Å</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=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [https://pdbe.org/1ppp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [https://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppp 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=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [https://pdbe.org/1ppp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [https://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppp 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=1ppp 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=1ppp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] were used for the structure solution and refinement. The papain structure was determined by means of the molecular replacement method, and then the inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference Fourier map. The complex structure was finally refined to R = 19.4% including 207 solvent molecules. Although this complex crystal (Form II) was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were significantly different from each other. By the calculation of accessible surface area for each complex atom, these two different binding modes were both shown to be tight enough to prevent the access of solvent molecules to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states which were derived from the crystal structures of Forms I and II. One of these, which corresponds to the binding mode simulated from Form I, was essentially the same as that observed in the crystal structure, and the other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the papain S subsites. The substrate specificity for the papain active site is discussed on the basis of the present results.
-
-	Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites.,Kim MJ, Yamamoto D, Matsumoto K, Inoue M, Ishida T, Mizuno H, Sumiya S, Kitamura K Biochem J. 1992 Nov 1;287 ( Pt 3):797-803. PMID:1445241<ref>PMID:1445241</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ppp" 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: Ishida T]]
-	[[Category: Ishida, T]]	+

OCA at 09:33, 8 September 2021

OCA — Wed, 08 Sep 2021 09:33:23 GMT

←Older revision		Revision as of 09:33, 8 September 2021
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	<StructureSection load='1ppp' size='340' side='right'caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ppp' size='340' side='right'caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Carpa Carpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppp]] 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=1PPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PPP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Papain Papain], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [~~http~~://pdbe.org/1ppp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppp 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=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [https://pdbe.org/1ppp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [https://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppp ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 10:17, 27 November 2019

OCA — Wed, 27 Nov 2019 10:17:55 GMT

←Older revision		Revision as of 10:17, 27 November 2019
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	==CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES==		==CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES==
-	<StructureSection load='1ppp' size='340' side='right' caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1ppp' size='340' side='right'caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carpa Carpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carpa Carpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1ppp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ppp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Papain\|Papain]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Carpa]]		[[Category: Carpa]]
		+	[[Category: Large Structures]]
	[[Category: Papain]]		[[Category: Papain]]
	[[Category: Ishida, T]]		[[Category: Ishida, T]]

OCA at 08:18, 24 February 2018

OCA — Sat, 24 Feb 2018 08:18:03 GMT

←Older revision		Revision as of 08:18, 24 February 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES==		==CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES==
	<StructureSection load='1ppp' size='340' side='right' caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ppp' size='340' side='right' caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://pdbe.org/1ppp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://pdbe.org/1ppp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ppp ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppp_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ 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=1ppp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1ppp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ppp" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Papain\|Papain]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:15, 11 September 2015

OCA — Fri, 11 Sep 2015 23:15:13 GMT

←Older revision		Revision as of 23:15, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ppp' size='340' side='right' caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ppp' size='340' side='right' caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Carica_papaya Carica papaya~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carpa Carpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://pdbe.org/1ppp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1ppp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carica papaya~~]]	+	[[Category: Carpa]]
	[[Category: Papain]]		[[Category: Papain]]
	[[Category: Ishida, T]]		[[Category: Ishida, T]]

OCA at 08:13, 6 January 2015

OCA — Tue, 06 Jan 2015 08:13:31 GMT

←Older revision		Revision as of 08:13, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Carica papaya]]		[[Category: Carica papaya]]
	[[Category: Papain]]		[[Category: Papain]]
-	[[Category: Ishida, T.]]	+	[[Category: Ishida, T]]

OCA at 21:56, 28 September 2014

OCA — Sun, 28 Sep 2014 21:56:01 GMT

←Older revision		Revision as of 21:56, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ppp.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES==
		+	<StructureSection load='1ppp' size='340' side='right' caption='[[1ppp]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PPP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ppp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ppp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ppp RCSB], [http://www.ebi.ac.uk/pdbsum/1ppp PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/1ppp_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In order to investigate the binding mode of E64-c (a synthetic cysteine proteinase inhibitor) to papain at the atomic level, the crystal structure of the complex was analysed by X-ray diffraction at 1.9 A (1 A is expressed in SI units as 0.1 nm) resolution. The crystal has a space group P2(1)2(1)2(1) with a = 43.37, b = 102.34 and c = 49.95 A. A total of 21,135 observed reflections were collected from the same crystal, and 14811 unique reflections of up to 1.9 A resolution [Fo > 3 sigma(Fo)] were used for the structure solution and refinement. The papain structure was determined by means of the molecular replacement method, and then the inhibitor was observed on a (2 magnitude of Fo-magnitude of Fc) difference Fourier map. The complex structure was finally refined to R = 19.4% including 207 solvent molecules. Although this complex crystal (Form II) was polymorphous as compared with the previously analysed one (Form I), the binding modes of leucine and isoamylamide moieties of E64-c were significantly different from each other. By the calculation of accessible surface area for each complex atom, these two different binding modes were both shown to be tight enough to prevent the access of solvent molecules to the papain active site. With respect to the E64-c-papain binding mode, molecular-dynamics simulations proposed two kinds of stationary states which were derived from the crystal structures of Forms I and II. One of these, which corresponds to the binding mode simulated from Form I, was essentially the same as that observed in the crystal structure, and the other was somewhat different from the crystal structure of Form II, especially with respect to the binding of the isoamylamide moiety with the papain S subsites. The substrate specificity for the papain active site is discussed on the basis of the present results.

-	~~{{STRUCTURE_1ppp\| PDB=1ppp \| SCENE= }}~~	+	Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites.,Kim MJ, Yamamoto D, Matsumoto K, Inoue M, Ishida T, Mizuno H, Sumiya S, Kitamura K Biochem J. 1992 Nov 1;287 ( Pt 3):797-803. PMID:1445241<ref>PMID:1445241</ref>

-	~~===CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1445241}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ppp]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Carica_papaya Carica papaya]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA].~~	+

	==See Also==		==See Also==
	*[[Papain\|Papain]]		*[[Papain\|Papain]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:001445241<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Carica papaya]]		[[Category: Carica papaya]]
	[[Category: Papain]]		[[Category: Papain]]
	[[Category: Ishida, T.]]		[[Category: Ishida, T.]]

OCA at 21:23, 20 October 2012

OCA — Sat, 20 Oct 2012 21:23:56 GMT

←Older revision		Revision as of 21:23, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ppp]] is a 1 chain structure ~~of [[Papain]]~~ with sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA].	+	[[1ppp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Carica_papaya Carica papaya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PPP OCA].

	==See Also==		==See Also==

OCA at 13:07, 27 July 2012

OCA — Fri, 27 Jul 2012 13:07:57 GMT

←Older revision		Revision as of 13:07, 27 July 2012
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	[[Image:1ppp.png\|left\|200px]]		[[Image:1ppp.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_1ppp\| PDB=1ppp \| SCENE= }}		{{STRUCTURE_1ppp\| PDB=1ppp \| SCENE= }}

	===CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES===		===CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1445241}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1445241 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_1445241}}		{{ABSTRACT_PUBMED_1445241}}

OCA: Protected "1ppp" [edit=sysop:move=sysop]

OCA — Wed, 09 May 2012 08:21:39 GMT

Protected "1ppp" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:21, 9 May 2012