5p13 - Revision history

OCA at 01:30, 28 December 2023

2023-12-28T01:30:45Z

←Older revision		Revision as of 01:30, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5P13 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5P13 FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.399Å</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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [https://pdbe.org/5p13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [https://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [https://pdbe.org/5p13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [https://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5p13" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5p13" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pepsin\|Pepsin]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
-	[[Category: Endothiapepsin]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Heine, A]]	+	[[Category: Heine A]]
-	[[Category: Klebe, G]]	+	[[Category: Klebe G]]
-	[[Category: Schiebel, J]]	+	[[Category: Schiebel J]]
-	~~[[Category: Aspartic protease]]~~	+
-	~~[[Category: Fragment screening]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Method development~~]]	+

OCA at 13:44, 17 November 2021

2021-11-17T13:44:20Z

←Older revision		Revision as of 13:44, 17 November 2021
Line 3:		Line 3:
	<StructureSection load='5p13' size='340' side='right'caption='[[5p13]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5p13' size='340' side='right'caption='[[5p13]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5P13 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5P13 FirstGlance]. <br>
-	</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>	+	</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~~://proteopedia.org/fgij/fg.htm?mol=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [~~http~~://pdbe.org/5p13 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [https://pdbe.org/5p13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [https://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:36, 2 September 2020

2020-09-02T07:36:53Z

←Older revision		Revision as of 07:36, 2 September 2020
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	==Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 86==		==Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 86==
-	<StructureSection load='5p13' size='340' side='right' caption='[[5p13]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5p13' size='340' side='right'caption='[[5p13]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5P13 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5P13 FirstGlance]. <br>
	</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>		</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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [http://pdbe.org/5p13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [http://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [http://pdbe.org/5p13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [http://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]
		+	[[Category: Large Structures]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]

OCA at 07:58, 10 August 2016

2016-08-10T07:58:15Z

←Older revision		Revision as of 07:58, 10 August 2016
Line 7:		Line 7:
	<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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [http://pdbe.org/5p13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [http://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [http://pdbe.org/5p13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [http://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that approximately 25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.
		+
		+	High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.,Schiebel J, Krimmer SG, Rower K, Knorlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glockner S, Weiss MS, Mueller U, Klebe G, Heine A Structure. 2016 Aug 2;24(8):1398-409. doi: 10.1016/j.str.2016.06.010. Epub 2016, Jul 21. PMID:27452405<ref>PMID:27452405</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5p13" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:27, 4 August 2016

2016-08-04T04:27:36Z

←Older revision		Revision as of 04:27, 4 August 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5p13 is ~~ON HOLD~~	+	==Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 86==
-		+	<StructureSection load='5p13' size='340' side='right' caption='[[5p13]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Schiebel~~, J., ~~Heine~~, A., ~~Klebe~~, G.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5p13]] 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=5P13 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5P13 FirstGlance]. <br>
-	~~Description~~: ~~Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 86~~	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5p13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p13 OCA], [http://pdbe.org/5p13 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5p13 RCSB], [http://www.ebi.ac.uk/pdbsum/5p13 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5p13 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cryphonectria parasitica]]
		+	[[Category: Endothiapepsin]]
		+	[[Category: Heine, A]]
		+	[[Category: Klebe, G]]
	[[Category: Schiebel, J]]		[[Category: Schiebel, J]]
-	[[Category: ~~Klebe, G~~]]	+	[[Category: Aspartic protease]]
-	[[Category: ~~Heine, A~~]]	+	[[Category: Fragment screening]]
		+	[[Category: Hydrolase]]
		+	[[Category: Method development]]

OCA: Protected "5p13" [edit=sysop:move=sysop]

2016-07-14T10:11:49Z

Protected "5p13" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:11, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5p13 is ON HOLD Authors: Schiebel, J., Heine, A., Klebe, G. Description: Automated refinement of diffraction data obtained from an endothiapepsin c...

2016-07-14T10:11:47Z

New page: '''Unreleased structure''' The entry 5p13 is ON HOLD Authors: Schiebel, J., Heine, A., Klebe, G. Description: Automated refinement of diffraction data obtained from an endothiapepsin c...

New page

'''Unreleased structure'''

The entry 5p13 is ON HOLD

Authors: Schiebel, J., Heine, A., Klebe, G.

Description: Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 86
[[Category: Unreleased Structures]]
[[Category: Schiebel, J]]
[[Category: Klebe, G]]
[[Category: Heine, A]]