1ent - Revision history

OCA at 10:04, 20 March 2024

OCA — Wed, 20 Mar 2024 10:04:25 GMT

←Older revision		Revision as of 10:04, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='1ent' size='340' side='right'caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ent' size='340' side='right'caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Crypa Crypa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ENT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ENT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Endothiapepsin Endothiapepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [https://pdbe.org/1ent PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [https://www.ebi.ac.uk/pdbsum/1ent PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ent 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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [https://pdbe.org/1ent PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [https://www.ebi.ac.uk/pdbsum/1ent PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ent ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 20:
	</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=1ent 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=1ent ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The molecular structure of endothiapepsin (EC 3.4.23.6), the aspartic proteinase from Endothia parasitica, has been refined to a crystallographic R-factor of 0.178 at 2.1 A resolution. The positions of 2389 protein non-hydrogen atoms have been determined and the present model contains 333 solvent molecules. The structure is bilobal, consisting of two predominantly beta-sheet domains that are related by an approximate 2-fold axis. Of approximately 170 residues, 65 are topologically equivalent when one lobe is superimposed on the other. Twenty beta-strands are arranged as five beta-sheets and are connected by regions involving 29 turns and four helices. A central sheet involves three antiparallel strands from each lobe organized around the dyad axis. Each lobe contains a further local dyad that passes through two sheets arranged as a sandwich and relates two equivalent motifs of four antiparallel strands (a, b, c, d) followed by a helix or an irregular helical region. Sheets 1N and 1C, each contain two interpenetrating psi structures contributed by strands c,d,d' and c',d',d, which are related by the intralobe dyad. A further sheet, 2N or 2C, is formed from two extended beta-hairpins from strands b,c and b',c' that fold above the sheets 1N and 1C, respectively, and are hydrogen-bonded around the local intralobe dyad. Asp32 and Asp215 are related by the interlobe dyad and form an intricate hydrogen-bonded network with the neighbouring residues and comprise the most symmetrical part of the structure. The side-chains of the active site aspartate residues are held coplanar and the nearby main chain makes a "fireman's grip" hydrogen-bonding network. Residues 74 to 83 from strands a'N and b'N in the N-terminal lobe form a beta-hairpin loop with high thermal parameters. This "flap" projects over the active site cleft and shields the active site from the solvent region. Shells of water molecules are found on the surface of the protein molecule and large solvent channels are observed within the crystal. There are only three regions of intermolecular contacts and the crystal packing is stabilized by many solvent molecules forming a network of hydrogen bonds. The three-dimensional structure of endothiapepsin is found to be similar to two other fungal aspartic proteinases, penicillopepsin and rhizopuspepsin. Even though sequence identities of endothiapepsin with rhizopuspepsin and penicillopepsin are only 41% and 51%, respectively, a superposition of the three-dimensional structures of these three enzymes shows that 237 residues (72%) are within a root-mean-square distance of 1.0 A.
-
-	X-ray analyses of aspartic proteinases. The three-dimensional structure at 2.1 A resolution of endothiapepsin.,Blundell TL, Jenkins JA, Sewell BT, Pearl LH, Cooper JB, Tickle IJ, Veerapandian B, Wood SP J Mol Biol. 1990 Feb 20;211(4):919-41. PMID:2179568<ref>PMID:2179568</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ent" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Pepsin\|Pepsin]]		*[[Pepsin\|Pepsin]]
-	*[[Proteinase\|Proteinase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Crypa]]~~	+	[[Category: Cryphonectria parasitica]]
-	~~[[Category: Endothiapepsin~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blundell~~, T L~~]]	+	[[Category: Blundell TL]]
-	[[Category: Dealwis~~, C G]]~~	+	[[Category: Dealwis CG]]
-	~~[[Category: Acid proteinase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 09:39, 21 July 2021

OCA — Wed, 21 Jul 2021 09:39:48 GMT

←Older revision		Revision as of 09:39, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1ent' size='340' side='right'caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ent' size='340' side='right'caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Crypa Crypa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ENT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Crypa Crypa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ENT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [~~http~~://pdbe.org/1ent PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ent PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ent 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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [https://pdbe.org/1ent PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [https://www.ebi.ac.uk/pdbsum/1ent PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ent ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:
	==See Also==		==See Also==
	*[[Pepsin\|Pepsin]]		*[[Pepsin\|Pepsin]]
		+	*[[Proteinase\|Proteinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:50, 16 October 2019

OCA — Wed, 16 Oct 2019 08:50:12 GMT

←Older revision		Revision as of 08:50, 16 October 2019
Line 1:		Line 1:

	==X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN==		==X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN==
-	<StructureSection load='1ent' size='340' side='right' caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1ent' size='340' side='right'caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Crypa Crypa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Crypa Crypa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/1ent_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/1ent_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>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1ent" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ent" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pepsin\|Pepsin]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	[[Category: Crypa]]		[[Category: Crypa]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]
		+	[[Category: Large Structures]]
	[[Category: Blundell, T L]]		[[Category: Blundell, T L]]
	[[Category: Dealwis, C G]]		[[Category: Dealwis, C G]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 06:32, 29 November 2017

OCA — Wed, 29 Nov 2017 06:32:52 GMT

←Older revision		Revision as of 06:32, 29 November 2017
Line 1:		Line 1:
		+
	==X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN==		==X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN==
	<StructureSection load='1ent' size='340' side='right' caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ent' size='340' side='right' caption='[[1ent]], [[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=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://pdbe.org/1ent PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent 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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://pdbe.org/1ent PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ent ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1ent" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ent" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Pepsin\|Pepsin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:30, 9 February 2016

OCA — Tue, 09 Feb 2016 00:30:45 GMT

←Older revision		Revision as of 00:30, 9 February 2016
Line 15:		Line 15:
	<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=1ent ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:51, 10 September 2015

OCA — Thu, 10 Sep 2015 16:51:17 GMT

←Older revision		Revision as of 16:51, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ent' size='340' side='right' caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1ent' size='340' side='right' caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cryphonectria_parasitica Cryphonectria parasitica~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Crypa Crypa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent 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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://pdbe.org/1ent PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1ent" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cryphonectria parasitica~~]]	+	[[Category: Crypa]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]
	[[Category: Blundell, T L]]		[[Category: Blundell, T L]]

OCA at 19:13, 22 December 2014

OCA — Mon, 22 Dec 2014 19:13:35 GMT

←Older revision		Revision as of 19:13, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent 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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent 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: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]
-	[[Category: Blundell, T L.]]	+	[[Category: Blundell, T L]]
-	[[Category: Dealwis, C G.]]	+	[[Category: Dealwis, C G]]
	[[Category: Acid proteinase]]		[[Category: Acid proteinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 11:16, 24 September 2014

OCA — Wed, 24 Sep 2014 11:16:23 GMT

←Older revision		Revision as of 11:16, 24 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1ent.~~png\|left~~\|200px]]	+	==X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN==
		+	<StructureSection load='1ent' size='340' side='right' caption='[[1ent]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ENT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0EM:N-(TERT-BUTOXYCARBONYL)-L-PHENYLALANYL-N-{(1S)-1-[(R)-HYDROXY(2-{[(2S)-2-METHYLBUTYL]AMINO}-2-OXOETHYL)PHOSPHORYL]-3-METHYLBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0EM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=1ent FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ent OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ent RCSB], [http://www.ebi.ac.uk/pdbsum/1ent 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/en/1ent_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 ==
		+	The molecular structure of endothiapepsin (EC 3.4.23.6), the aspartic proteinase from Endothia parasitica, has been refined to a crystallographic R-factor of 0.178 at 2.1 A resolution. The positions of 2389 protein non-hydrogen atoms have been determined and the present model contains 333 solvent molecules. The structure is bilobal, consisting of two predominantly beta-sheet domains that are related by an approximate 2-fold axis. Of approximately 170 residues, 65 are topologically equivalent when one lobe is superimposed on the other. Twenty beta-strands are arranged as five beta-sheets and are connected by regions involving 29 turns and four helices. A central sheet involves three antiparallel strands from each lobe organized around the dyad axis. Each lobe contains a further local dyad that passes through two sheets arranged as a sandwich and relates two equivalent motifs of four antiparallel strands (a, b, c, d) followed by a helix or an irregular helical region. Sheets 1N and 1C, each contain two interpenetrating psi structures contributed by strands c,d,d' and c',d',d, which are related by the intralobe dyad. A further sheet, 2N or 2C, is formed from two extended beta-hairpins from strands b,c and b',c' that fold above the sheets 1N and 1C, respectively, and are hydrogen-bonded around the local intralobe dyad. Asp32 and Asp215 are related by the interlobe dyad and form an intricate hydrogen-bonded network with the neighbouring residues and comprise the most symmetrical part of the structure. The side-chains of the active site aspartate residues are held coplanar and the nearby main chain makes a "fireman's grip" hydrogen-bonding network. Residues 74 to 83 from strands a'N and b'N in the N-terminal lobe form a beta-hairpin loop with high thermal parameters. This "flap" projects over the active site cleft and shields the active site from the solvent region. Shells of water molecules are found on the surface of the protein molecule and large solvent channels are observed within the crystal. There are only three regions of intermolecular contacts and the crystal packing is stabilized by many solvent molecules forming a network of hydrogen bonds. The three-dimensional structure of endothiapepsin is found to be similar to two other fungal aspartic proteinases, penicillopepsin and rhizopuspepsin. Even though sequence identities of endothiapepsin with rhizopuspepsin and penicillopepsin are only 41% and 51%, respectively, a superposition of the three-dimensional structures of these three enzymes shows that 237 residues (72%) are within a root-mean-square distance of 1.0 A.

-	~~{{STRUCTURE_1ent\| PDB=1ent \| SCENE= }}~~	+	X-ray analyses of aspartic proteinases. The three-dimensional structure at 2.1 A resolution of endothiapepsin.,Blundell TL, Jenkins JA, Sewell BT, Pearl LH, Cooper JB, Tickle IJ, Veerapandian B, Wood SP J Mol Biol. 1990 Feb 20;211(4):919-41. PMID:2179568<ref>PMID:2179568</ref>

-	~~===X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_2179568}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ent]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA].~~	+

	==See Also==		==See Also==
	*[[Pepsin\|Pepsin]]		*[[Pepsin\|Pepsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:002179568<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]

OCA at 12:00, 20 October 2012

OCA — Sat, 20 Oct 2012 12:00:21 GMT

←Older revision		Revision as of 12:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ent]] is a 1 chain structure ~~of [[Pepsin]]~~ with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA].	+	[[1ent]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ENT OCA].

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

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

OCA — Thu, 26 Jul 2012 07:18:25 GMT

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

←Older revision

Revision as of 07:18, 26 July 2012