7nge - Revision history

OCA at 12:34, 1 February 2024

OCA — Thu, 01 Feb 2024 12:34:41 GMT

←Older revision		Revision as of 12:34, 1 February 2024
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	<StructureSection load='7nge' size='340' side='right'caption='[[7nge]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='7nge' size='340' side='right'caption='[[7nge]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7nge]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nge]] 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=7NGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NGE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NFK:N-FORMYLKYNURENINE'>NFK</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NFK:N-FORMYLKYNURENINE'>NFK</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=7nge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nge OCA], [https://pdbe.org/7nge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nge RCSB], [https://www.ebi.ac.uk/pdbsum/7nge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nge 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=7nge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nge OCA], [https://pdbe.org/7nge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nge RCSB], [https://www.ebi.ac.uk/pdbsum/7nge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nge ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN]] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>	+	[https://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>
	<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 7nge" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7nge" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Indoleamine 2,3-dioxygenase~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mirgaux, M]]	+	[[Category: Mirgaux M]]
-	[[Category: Wouters, J]]	+	[[Category: Wouters J]]
-	~~[[Category: Dynamics loop]]~~	+
-	~~[[Category: Hemoprotein]]~~	+
-	~~[[Category: L-trp metabolism]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:45, 5 January 2022

OCA — Wed, 05 Jan 2022 10:45:13 GMT

←Older revision		Revision as of 10:45, 5 January 2022
Line 1:		Line 1:

	==Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation==		==Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation==
-	<StructureSection load='7nge' size='340' side='right'caption='[[7nge]]' scene=''>	+	<StructureSection load='7nge' size='340' side='right'caption='[[7nge]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NGE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7nge]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NGE FirstGlance]. <br>
-	</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=7nge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nge OCA], [https://pdbe.org/7nge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nge RCSB], [https://www.ebi.ac.uk/pdbsum/7nge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nge ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NFK:N-FORMYLKYNURENINE'>NFK</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </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=7nge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nge OCA], [https://pdbe.org/7nge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nge RCSB], [https://www.ebi.ac.uk/pdbsum/7nge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nge ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN]] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein dynamics governs most of the fundamental processes in the human body. Particularly, the dynamics of loops located near an active site can be involved in the positioning of the substrate and the reaction mechanism. The understanding of the functioning of dynamic loops is therefore a challenge, and often requires the use of a multi-disciplinary approach mixing, for example, crystallographic experiments and molecular dynamics simulations. In the present work, the dynamic behavior of the JK-loop of the human indoleamine 2,3-dioxygenase 1 hemoprotein, a target for immunotherapy, is investigated. To overcome the lack of knowledge on this dynamism, the study reported here is based on 3 crystal structures presenting different conformations of the loop, completed with molecular dynamics trajectories and MM-GBSA analyses, in order to trace the reaction pathway of the enzyme. In addition, the crystal structures identify an exo site in the small unit of the enzyme, that is populated redundantly by the substrate or the product of the reaction. The role of this newer reported exo site still needs to be investigated.
		+
		+	Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site.,Mirgaux M, Leherte L, Wouters J Int J Tryptophan Res. 2021 Dec 15;14:11786469211052964. doi:, 10.1177/11786469211052964. eCollection 2021. PMID:34949925<ref>PMID:34949925</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7nge" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Indoleamine 2,3-dioxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Mirgaux M]]	+	[[Category: Mirgaux, M]]
-	[[Category: Wouters J]]	+	[[Category: Wouters, J]]
		+	[[Category: Dynamics loop]]
		+	[[Category: Hemoprotein]]
		+	[[Category: L-trp metabolism]]
		+	[[Category: Oxidoreductase]]

OCA at 14:10, 29 December 2021

OCA — Wed, 29 Dec 2021 14:10:20 GMT

←Older revision		Revision as of 14:10, 29 December 2021
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-	'''Unreleased structure'''

-	~~The entry 7nge is ON HOLD until Paper Publication~~	+	==Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation==
-		+	<StructureSection load='7nge' size='340' side='right'caption='[[7nge]]' scene=''>
-	~~Authors: Mirgaux, M., Wouters, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NGE FirstGlance]. <br>
-	~~Description:~~ Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation	+	</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=7nge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nge OCA], [https://pdbe.org/7nge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nge RCSB], [https://www.ebi.ac.uk/pdbsum/7nge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nge ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Wouters~~, J]]	+	__TOC__
-	[[Category: Mirgaux, M]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mirgaux M]]
		+	[[Category: Wouters J]]

OCA at 13:31, 3 March 2021

OCA — Wed, 03 Mar 2021 13:31:37 GMT

←Older revision		Revision as of 13:31, 3 March 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7nge is ON HOLD	+	The entry 7nge is ON HOLD until Paper Publication

	Authors: Mirgaux, M., Wouters, J.		Authors: Mirgaux, M., Wouters, J.

OCA: Protected "7nge" [edit=sysop:move=sysop]

OCA — Wed, 17 Feb 2021 08:55:26 GMT

Protected "7nge" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:55, 17 February 2021

OCA: New page: '''Unreleased structure''' The entry 7nge is ON HOLD Authors: Mirgaux, M., Wouters, J. Description: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the J...

OCA — Wed, 17 Feb 2021 08:55:25 GMT

New page: '''Unreleased structure''' The entry 7nge is ON HOLD Authors: Mirgaux, M., Wouters, J. Description: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the J...

New page

'''Unreleased structure'''

The entry 7nge is ON HOLD

Authors: Mirgaux, M., Wouters, J.

Description: Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation
[[Category: Unreleased Structures]]
[[Category: Wouters, J]]
[[Category: Mirgaux, M]]