5k1v - Revision history

OCA at 19:18, 20 September 2023

OCA — Wed, 20 Sep 2023 19:18:19 GMT

←Older revision		Revision as of 19:18, 20 September 2023
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	<StructureSection load='5k1v' size='340' side='right'caption='[[5k1v]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5k1v' size='340' side='right'caption='[[5k1v]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k1v]] is a 2 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=5K1V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k1v]] is a 2 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=5K1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K1V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PX:METHYL+N-[4-AMINO-3-(L-ARGINYLAMINO)BENZENE-1-CARBONYL]-L-TYROSINATE'>6PX</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.897Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERAP2, LRAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PX:METHYL+N-[4-AMINO-3-(L-ARGINYLAMINO)BENZENE-1-CARBONYL]-L-TYROSINATE'>6PX</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5k1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1v OCA], [~~http~~://pdbe.org/5k1v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k1v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k1v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1v 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=5k1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1v OCA], [https://pdbe.org/5k1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k1v RCSB], [https://www.ebi.ac.uk/pdbsum/5k1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ERAP2_HUMAN ERAP2_HUMAN]] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Preferentially hydrolyzes the basic residues Arg and Lys.<ref>PMID:12799365</ref> <ref>PMID:15908954</ref> <ref>PMID:16286653</ref>	+	[https://www.uniprot.org/uniprot/ERAP2_HUMAN ERAP2_HUMAN] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Preferentially hydrolyzes the basic residues Arg and Lys.<ref>PMID:12799365</ref> <ref>PMID:15908954</ref> <ref>PMID:16286653</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Giastas, P]]	+	[[Category: Giastas P]]
-	[[Category: Mavridis~~, I M~~]]	+	[[Category: Mavridis IM]]
-	[[Category: Mpakali, A]]	+	[[Category: Mpakali A]]
-	[[Category: Papakyriakou, A]]	+	[[Category: Papakyriakou A]]
-	[[Category: Saridakis, E]]	+	[[Category: Saridakis E]]
-	[[Category: Stratikos, E]]	+	[[Category: Stratikos E]]
-	~~[[Category: Diaminobenzoic acid derivative]]~~	+
-	~~[[Category: Endoplasmic reticulum aminopeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Zinc-binding metallopeptidase~~]]	+

OCA at 09:14, 25 June 2020

OCA — Thu, 25 Jun 2020 09:14:26 GMT

←Older revision		Revision as of 09:14, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.==		==Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.==
-	<StructureSection load='5k1v' size='340' side='right' caption='[[5k1v]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5k1v' size='340' side='right'caption='[[5k1v]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k1v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k1v]] is a 2 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=5K1V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K1V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6PX:METHYL+N-[4-AMINO-3-(L-ARGINYLAMINO)BENZENE-1-CARBONYL]-L-TYROSINATE'>6PX</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6PX:METHYL+N-[4-AMINO-3-(L-ARGINYLAMINO)BENZENE-1-CARBONYL]-L-TYROSINATE'>6PX</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5k1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1v OCA], [http://pdbe.org/5k1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k1v RCSB], [http://www.ebi.ac.uk/pdbsum/5k1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1v ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERAP2, LRAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5k1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1v OCA], [http://pdbe.org/5k1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k1v RCSB], [http://www.ebi.ac.uk/pdbsum/5k1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5k1v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k1v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Giastas, P]]		[[Category: Giastas, P]]
	[[Category: Mavridis, I M]]		[[Category: Mavridis, I M]]

OCA at 06:41, 5 April 2017

OCA — Wed, 05 Apr 2017 06:41:54 GMT

←Older revision		Revision as of 06:41, 5 April 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ERAP2_HUMAN ERAP2_HUMAN]] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Preferentially hydrolyzes the basic residues Arg and Lys.<ref>PMID:12799365</ref> <ref>PMID:15908954</ref> <ref>PMID:16286653</ref>		[[http://www.uniprot.org/uniprot/ERAP2_HUMAN ERAP2_HUMAN]] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Preferentially hydrolyzes the basic residues Arg and Lys.<ref>PMID:12799365</ref> <ref>PMID:15908954</ref> <ref>PMID:16286653</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses. To better understand the structural elements of inhibitors that govern their binding affinity to the ERAP2 active site, we cocrystallized ERAP2 with a medium activity 3,4-diaminobenzoic acid inhibitor and a poorly active hydroxamic acid derivative. Comparison of these two crystal structures with a previously solved structure of ERAP2 in complex with a potent phosphinic pseudopeptide inhibitor suggests that engaging the substrate N-terminus recognition properties of the active site is crucial for inhibitor binding even in the absence of a potent zinc-binding group. Proper utilization of all five major pharmacophores is necessary, however, to optimize inhibitor potency.
		+
		+	Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements for Optimizing Inhibitor Potency.,Mpakali A, Giastas P, Deprez-Poulain R, Papakyriakou A, Koumantou D, Gealageas R, Tsoukalidou S, Vourloumis D, Mavridis IM, Stratikos E, Saridakis E ACS Med Chem Lett. 2017 Feb 21;8(3):333-337. doi: 10.1021/acsmedchemlett.6b00505., eCollection 2017 Mar 9. PMID:28337326<ref>PMID:28337326</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k1v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:46, 29 March 2017

OCA — Wed, 29 Mar 2017 13:46:09 GMT

←Older revision		Revision as of 13:46, 29 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5k1v is ON HOLD until Paper Publication~~	+	==Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.==
-		+	<StructureSection load='5k1v' size='340' side='right' caption='[[5k1v]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~Authors: Saridakis, E., Papakyriakou, A., Giastas, P., Mpakali, A., Mavridis, I.M., Stratikos, E.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5k1v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K1V FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6PX:METHYL+N-[4-AMINO-3-(L-ARGINYLAMINO)BENZENE-1-CARBONYL]-L-TYROSINATE'>6PX</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5k1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1v OCA], [http://pdbe.org/5k1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k1v RCSB], [http://www.ebi.ac.uk/pdbsum/5k1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1v ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Saridakis, E~~]]	+	</table>
-	[[~~Category~~: ~~Papakyriakou~~, A]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ERAP2_HUMAN ERAP2_HUMAN]] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Preferentially hydrolyzes the basic residues Arg and Lys.<ref>PMID:12799365</ref> <ref>PMID:15908954</ref> <ref>PMID:16286653</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Giastas, P]]		[[Category: Giastas, P]]
		+	[[Category: Mavridis, I M]]
	[[Category: Mpakali, A]]		[[Category: Mpakali, A]]
		+	[[Category: Papakyriakou, A]]
		+	[[Category: Saridakis, E]]
	[[Category: Stratikos, E]]		[[Category: Stratikos, E]]
-	[[Category: ~~Mavridis, I.M~~]]	+	[[Category: Diaminobenzoic acid derivative]]
		+	[[Category: Endoplasmic reticulum aminopeptidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Zinc-binding metallopeptidase]]

OCA at 10:07, 9 March 2017

OCA — Thu, 09 Mar 2017 10:07:59 GMT

←Older revision		Revision as of 10:07, 9 March 2017
Line 7:		Line 7:
	Description: Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.		Description: Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Giastas, P]]
-	[[Category: Stratikos, E]]
-	[[Category: Mavridis, I.M]]
	[[Category: Saridakis, E]]		[[Category: Saridakis, E]]
	[[Category: Papakyriakou, A]]		[[Category: Papakyriakou, A]]
		+	[[Category: Giastas, P]]
	[[Category: Mpakali, A]]		[[Category: Mpakali, A]]
		+	[[Category: Stratikos, E]]
		+	[[Category: Mavridis, I.M]]

OCA: Protected "5k1v" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:12:16 GMT

Protected "5k1v" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:12, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k1v is ON HOLD until Paper Publication Authors: Saridakis, E., Papakyriakou, A., Giastas, P., Mpakali, A., Mavridis, I.M., Stratikos, E. Descripti...

OCA — Wed, 01 Jun 2016 14:12:15 GMT

New page: '''Unreleased structure''' The entry 5k1v is ON HOLD until Paper Publication Authors: Saridakis, E., Papakyriakou, A., Giastas, P., Mpakali, A., Mavridis, I.M., Stratikos, E. Descripti...

New page

'''Unreleased structure'''

The entry 5k1v is ON HOLD until Paper Publication

Authors: Saridakis, E., Papakyriakou, A., Giastas, P., Mpakali, A., Mavridis, I.M., Stratikos, E.

Description: Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.
[[Category: Unreleased Structures]]
[[Category: Giastas, P]]
[[Category: Stratikos, E]]
[[Category: Mavridis, I.M]]
[[Category: Saridakis, E]]
[[Category: Papakyriakou, A]]
[[Category: Mpakali, A]]