4mny - Revision history

OCA at 09:55, 28 December 2022

2022-12-28T09:55:02Z

←Older revision		Revision as of 09:55, 28 December 2022
Line 1:		Line 1:

	==Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903==		==Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903==
-	<StructureSection load='4mny' size='340' side='right' caption='[[4mny]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4mny' size='340' side='right'caption='[[4mny]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mny]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MNY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mny]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MNY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=29O:N,N,N-BENZENE-1,3,5-TRIYLTRIS(2-BROMOACETAMIDE)'>29O</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=29O:N,N,N-BENZENE-1,3,5-TRIYLTRIS(2-BROMOACETAMIDE)'>29O</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~NH2~~:~~AMINO~~+~~GROUP~~'>~~NH2~~</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=4mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mny OCA], [https://pdbe.org/4mny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mny RCSB], [https://www.ebi.ac.uk/pdbsum/4mny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mny ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mnv\|4mnv]], [[4mnw\|4mnw]], [[4mnx\|4mnx]], [[3qn7\|3qn7]], [[2nwn\|2nwn]], [[4jk5\|4jk5]], [[4jk6\|4jk6]], [[4gly\|4gly]]</td></tr>	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLAU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/U-plasminogen_activator U-plasminogen activator], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.73 3.4.21.73] </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=4mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mny OCA], [~~http~~://pdbe.org/4mny PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mny RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mny PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mny ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[~~http~~://omim.org/entry/601709 601709]]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>	+	[https://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[https://omim.org/entry/601709 601709]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.	+	[https://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4mny" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4mny" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Plasminogen activator\|Plasminogen activator]]
		+	*[[Urokinase 3D Structures\|Urokinase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~U-plasminogen activator~~]]	+	[[Category: Large Structures]]
-	[[Category: Chen, S]]	+	[[Category: Chen S]]
-	[[Category: Heinis, C]]	+	[[Category: Heinis C]]
-	[[Category: Pojer, F]]	+	[[Category: Pojer F]]
-	~~[[Category: Bicyclic peptide]]~~	+
-	~~[[Category: Competitive inhibitor]]~~	+
-	~~[[Category: Extracellular]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Ns']]~~	+
-	~~[[Category: Protease~~]]	+

OCA at 09:54, 15 November 2017

2017-11-15T09:54:37Z

←Older revision		Revision as of 09:54, 15 November 2017
Line 24:		Line 24:
	</div>		</div>
	<div class="pdbe-citations 4mny" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4mny" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Urokinase\|Urokinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:19, 11 August 2016

2016-08-11T19:19:52Z

←Older revision		Revision as of 19:19, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903==		==Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903==
	<StructureSection load='4mny' size='340' side='right' caption='[[4mny]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4mny' size='340' side='right' caption='[[4mny]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLAU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLAU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/U-plasminogen_activator U-plasminogen activator], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.73 3.4.21.73] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/U-plasminogen_activator U-plasminogen activator], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.73 3.4.21.73] </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=4mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mny RCSB], [http://www.ebi.ac.uk/pdbsum/4mny 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=4mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mny OCA], [http://pdbe.org/4mny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mny RCSB], [http://www.ebi.ac.uk/pdbsum/4mny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mny ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 23:
	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 4mny" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Urokinase\|Urokinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:41, 20 January 2015

2015-01-20T09:41:59Z

←Older revision		Revision as of 09:41, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4mny\| PDB=4mny \| SCENE= }}~~	+	==Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903==
-	===Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903===	+	<StructureSection load='4mny' size='340' side='right' caption='[[4mny]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24453110}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4mny]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MNY FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=29O:N,N,N-BENZENE-1,3,5-TRIYLTRIS(2-BROMOACETAMIDE)'>29O</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4mnv\|4mnv]], [[4mnw\|4mnw]], [[4mnx\|4mnx]], [[3qn7\|3qn7]], [[2nwn\|2nwn]], [[4jk5\|4jk5]], [[4jk6\|4jk6]], [[4gly\|4gly]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PLAU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/U-plasminogen_activator U-plasminogen activator], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.73 3.4.21.73] </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=4mny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mny RCSB], [http://www.ebi.ac.uk/pdbsum/4mny PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[http://omim.org/entry/601709 601709]]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>		[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[http://omim.org/entry/601709 601709]]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>
-		+	== Function ==
-	==Function==	+
	[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.		[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bicyclic peptides generated through directed evolution by using phage display offer an attractive ligand format for the development of therapeutics. Being nearly 100-fold smaller than antibodies, they promise advantages such as access to chemical synthesis, efficient diffusion into tissues, and needle-free application. However, unlike antibodies, they do not have a folded structure in solution and thus bind less well. We developed bicyclic peptides with hydrophilic chemical structures at their center to promote noncovalent intramolecular interactions, thereby stabilizing the peptide conformation. The sequences of the peptides isolated by phage display from large combinatorial libraries were strongly influenced by the type of small molecule used in the screen, thus suggesting that the peptides fold around the small molecules. X-ray structure analysis revealed that the small molecules indeed formed hydrogen bonds with the peptides. These noncovalent interactions stabilize the peptide-protein complexes and contribute to the high binding affinity.

-	~~==About this Structure==~~	+	Peptide ligands stabilized by small molecules.,Chen S, Bertoldo D, Angelini A, Pojer F, Heinis C Angew Chem Int Ed Engl. 2014 Feb 3;53(6):1602-6. doi: 10.1002/anie.201309459., Epub 2014 Jan 22. PMID:24453110<ref>PMID:24453110</ref>
-	~~[[4mny]] is a 4 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4MNY OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024453110</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
	[[Category: U-plasminogen activator]]		[[Category: U-plasminogen activator]]
-	[[Category: Chen, S.]]	+	[[Category: Chen, S]]
-	[[Category: Heinis, C.]]	+	[[Category: Heinis, C]]
-	[[Category: Pojer, F.]]	+	[[Category: Pojer, F]]
	[[Category: Bicyclic peptide]]		[[Category: Bicyclic peptide]]
	[[Category: Competitive inhibitor]]		[[Category: Competitive inhibitor]]

OCA at 11:16, 5 February 2014

2014-02-05T11:16:39Z

←Older revision		Revision as of 11:16, 5 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4mny\| PDB=4mny \| SCENE= }}
		+	===Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903===
		+	{{ABSTRACT_PUBMED_24453110}}

-	~~The~~ entry ~~4mny~~ is ~~ON HOLD~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[http://omim.org/entry/601709 601709]]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>

-	~~Authors~~: ~~Chen, S~~.~~, Pojer, F~~.~~, Heinis, C~~.	+	==Function==
		+	[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.

-	~~Description: Crystal~~ structure ~~of urokinase~~-~~type~~ plasminogen activator ~~(uPA) complexed with bicyclic~~ peptide ~~UK903~~	+	==About this Structure==
		+	[[4mny]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MNY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024453110</ref><references group="xtra"/><references/>
		+	[[Category: U-plasminogen activator]]
		+	[[Category: Chen, S.]]
		+	[[Category: Heinis, C.]]
		+	[[Category: Pojer, F.]]
		+	[[Category: Bicyclic peptide]]
		+	[[Category: Competitive inhibitor]]
		+	[[Category: Extracellular]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Ns']]
		+	[[Category: Protease]]

OCA: Protected "4mny" [edit=sysop:move=sysop]

2013-09-20T03:44:01Z

Protected "4mny" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:44, 20 September 2013

OCA: New page: '''Unreleased structure''' The entry 4mny is ON HOLD Authors: Chen, S., Pojer, F., Heinis, C. Description: Crystal structure of urokinase-type plasminogen activator (uPA) complexed wit...

2013-09-20T03:44:00Z

New page: '''Unreleased structure''' The entry 4mny is ON HOLD Authors: Chen, S., Pojer, F., Heinis, C. Description: Crystal structure of urokinase-type plasminogen activator (uPA) complexed wit...

New page

'''Unreleased structure'''

The entry 4mny is ON HOLD

Authors: Chen, S., Pojer, F., Heinis, C.

Description: Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic peptide UK903