7pfs - Revision history

OCA at 13:05, 1 February 2024

OCA — Thu, 01 Feb 2024 13:05:05 GMT

←Older revision		Revision as of 13:05, 1 February 2024
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	<StructureSection load='7pfs' size='340' side='right'caption='[[7pfs]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='7pfs' size='340' side='right'caption='[[7pfs]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7pfs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PFS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pfs]] 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=7PFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PFS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7OO:[(2~{S})-3-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-2-[(3,5-diphenylphenyl)methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic+acid'>7OO</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5ab0\|5ab0]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7OO:[(2~{S})-3-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-2-[(3,5-diphenylphenyl)methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic+acid'>7OO</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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'>[https://proteopedia.org/fgij/fg.htm?mol=7pfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pfs OCA], [https://pdbe.org/7pfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pfs RCSB], [https://www.ebi.ac.uk/pdbsum/7pfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pfs 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=7pfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pfs OCA], [https://pdbe.org/7pfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pfs RCSB], [https://www.ebi.ac.uk/pdbsum/7pfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pfs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7pfs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7pfs" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Giastas, P]]	+	[[Category: Giastas P]]
-	[[Category: Mpakali, A]]	+	[[Category: Mpakali A]]
-	[[Category: Stratikos, E]]	+	[[Category: Stratikos E]]
-	~~[[Category: Aminopeptidase]]~~	+
-	~~[[Category: Antigen presentation]]~~	+
-	~~[[Category: Erap2]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phosphinic pseudotripeptide]]~~	+
-	~~[[Category: Transition state analogue~~]]	+

OCA at 07:31, 2 March 2022

OCA — Wed, 02 Mar 2022 07:31:16 GMT

←Older revision		Revision as of 07:31, 2 March 2022
Line 1:		Line 1:

	==Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid==		==Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid==
-	<StructureSection load='7pfs' size='340' side='right'caption='[[7pfs]]' scene=''>	+	<StructureSection load='7pfs' size='340' side='right'caption='[[7pfs]], [[Resolution\|resolution]] 2.70Å' 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=7PFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PFS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pfs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PFS 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=7pfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pfs OCA], [https://pdbe.org/7pfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pfs RCSB], [https://www.ebi.ac.uk/pdbsum/7pfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pfs 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=7OO:[(2~{S})-3-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-2-[(3,5-diphenylphenyl)methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic+acid'>7OO</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5ab0\|5ab0]]</div></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=7pfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pfs OCA], [https://pdbe.org/7pfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pfs RCSB], [https://www.ebi.ac.uk/pdbsum/7pfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pfs ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[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;">
		+	== Publication Abstract from PubMed ==
		+	Endoplasmic reticulum aminopeptidase 2 (ERAP2) is an intracellular enzyme involved in the processing of antigenic peptides intended for presentation by major histocompatibility complex class I (MHCI) molecules. Because of its role in regulating immune responses, ERAP2 is an emerging pharmacological target. Phosphinic pseudopeptides are potent transition-state analogue inhibitors of ERAP2. Previous structure-activity studies have revealed a complex but ambiguous relationship between the occupation of putative specificity pockets and the inhibitor efficacy. To address these problems, we solved crystal structures of ERAP2 in complex with two phosphinic pseudotripeptide inhibitors. Both compounds are found in the catalytic site in a canonical orientation for transition-state analogues and utilize the S1 and S2' pockets in a similar fashion. Strikingly, their P1' side chains exhibit different orientations and make interactions with distinct shallow pockets near the ERAP2 active site. These structures suggest that S1' pocket usage in ERAP2 may be inhibitor-dependent and constitute useful starting templates for the further optimization of this class of compounds.
		+
		+	Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2.,Mpakali A, Georgiadis D, Stratikos E, Giastas P ACS Med Chem Lett. 2022 Jan 13;13(2):218-224. doi:, 10.1021/acsmedchemlett.1c00582. eCollection 2022 Feb 10. PMID:35178178<ref>PMID:35178178</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pfs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Giastas P]]	+	[[Category: Giastas, P]]
-	[[Category: Mpakali A]]	+	[[Category: Mpakali, A]]
-	[[Category: Stratikos E]]	+	[[Category: Stratikos, E]]
		+	[[Category: Aminopeptidase]]
		+	[[Category: Antigen presentation]]
		+	[[Category: Erap2]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphinic pseudotripeptide]]
		+	[[Category: Transition state analogue]]

OCA at 07:02, 27 January 2022

OCA — Thu, 27 Jan 2022 07:02:34 GMT

←Older revision		Revision as of 07:02, 27 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7pfs is ON HOLD until Paper Publication~~	+	==Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid==
-		+	<StructureSection load='7pfs' size='340' side='right'caption='[[7pfs]]' scene=''>
-	~~Authors: Giastas, P., Stratikos, E., Mpakali, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PFS FirstGlance]. <br>
-	~~Description:~~ Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid	+	</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=7pfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pfs OCA], [https://pdbe.org/7pfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pfs RCSB], [https://www.ebi.ac.uk/pdbsum/7pfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pfs ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Mpakali~~, A]]	+	__TOC__
-	[[Category: ~~Stratikos, E~~]]	+	</StructureSection>
-	[[Category: Giastas, P]]	+	[[Category: Large Structures]]
		+	[[Category: Giastas P]]
		+	[[Category: Mpakali A]]
		+	[[Category: Stratikos E]]

OCA at 07:30, 8 September 2021

OCA — Wed, 08 Sep 2021 07:30:35 GMT

←Older revision		Revision as of 07:30, 8 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Giastas, P., Stratikos, E., Mpakali, A.		Authors: Giastas, P., Stratikos, E., Mpakali, A.

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

OCA — Wed, 18 Aug 2021 05:04:21 GMT

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

←Older revision

Revision as of 05:04, 18 August 2021

OCA: New page: '''Unreleased structure''' The entry 7pfs is ON HOLD Authors: Giastas, P., Stratikos, E., Mpakali, A. Description: Crystal structure of ERAP2 aminopeptidase in complex with phosphinic ...

OCA — Wed, 18 Aug 2021 05:04:20 GMT

New page: '''Unreleased structure''' The entry 7pfs is ON HOLD Authors: Giastas, P., Stratikos, E., Mpakali, A. Description: Crystal structure of ERAP2 aminopeptidase in complex with phosphinic ...

New page

'''Unreleased structure'''

The entry 7pfs is ON HOLD

Authors: Giastas, P., Stratikos, E., Mpakali, A.

Description: Crystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid
[[Category: Unreleased Structures]]
[[Category: Mpakali, A]]
[[Category: Stratikos, E]]
[[Category: Giastas, P]]