5e33 - Revision history

OCA at 06:11, 5 July 2023

OCA — Wed, 05 Jul 2023 06:11:25 GMT

←Older revision		Revision as of 06:11, 5 July 2023
Line 3:		Line 3:
	<StructureSection load='5e33' size='340' side='right'caption='[[5e33]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5e33' size='340' side='right'caption='[[5e33]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e33]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E33 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5E33 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e33]] 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=5E33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5E33 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.837Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[3fvy\|3fvy]], [[3t6b\|3t6b]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_III Dipeptidyl-peptidase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.4 3.4.14.4]~~ </~~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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [https://pdbe.org/5e33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [https://www.ebi.ac.uk/pdbsum/5e33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5e33 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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [~~http~~://pdbe.org/5e33 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5e33 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5e33 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPP3_HUMAN DPP3_HUMAN]] Cleaves Arg-Arg-beta-naphthylamide.	+	[https://www.uniprot.org/uniprot/DPP3_HUMAN DPP3_HUMAN] Cleaves Arg-Arg-beta-naphthylamide.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dipeptidyl-peptidase III~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gruber, K]]	+	[[Category: Gruber K]]
-	[[Category: Kumar, P]]	+	[[Category: Kumar P]]
-	[[Category: Macheroux, P]]	+	[[Category: Macheroux P]]
-	[[Category: Pavkov-Keller, T]]	+	[[Category: Pavkov-Keller T]]
-	[[Category: Reisinger, M]]	+	[[Category: Reisinger M]]
-	[[Category: Reithofer, V]]	+	[[Category: Reithofer V]]
-	[[Category: Wallner, S]]	+	[[Category: Wallner S]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Opioid-peptide]]~~	+
-	~~[[Category: Peptidase]]~~	+
-	~~[[Category: Zinc-hydrolase~~]]	+

OCA at 06:41, 22 April 2020

OCA — Wed, 22 Apr 2020 06:41:56 GMT

←Older revision		Revision as of 06:41, 22 April 2020
Line 1:		Line 1:

	==Structure of human DPP3 in complex with met-enkephalin==		==Structure of human DPP3 in complex with met-enkephalin==
-	<StructureSection load='5e33' size='340' side='right' caption='[[5e33]], [[Resolution\|resolution]] 1.84Å' scene=''>	+	<StructureSection load='5e33' size='340' side='right'caption='[[5e33]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5e33]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E33 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5E33 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5e33]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E33 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5E33 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fvy\|3fvy]], [[3t6b\|3t6b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fvy\|3fvy]], [[3t6b\|3t6b]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_III Dipeptidyl-peptidase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.4 3.4.14.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_III Dipeptidyl-peptidase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.4 3.4.14.4] </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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [http://pdbe.org/5e33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [http://www.ebi.ac.uk/pdbsum/5e33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e33 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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [http://pdbe.org/5e33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [http://www.ebi.ac.uk/pdbsum/5e33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e33 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Dipeptidyl peptidase\|Dipeptidyl peptidase]]	+	*[[Dipeptidyl peptidase 3D structures\|Dipeptidyl peptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Dipeptidyl-peptidase III]]		[[Category: Dipeptidyl-peptidase III]]
		+	[[Category: Large Structures]]
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]

OCA at 03:42, 6 September 2017

OCA — Wed, 06 Sep 2017 03:42:57 GMT

←Older revision		Revision as of 03:42, 6 September 2017
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fvy\|3fvy]], [[3t6b\|3t6b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fvy\|3fvy]], [[3t6b\|3t6b]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_III Dipeptidyl-peptidase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.4 3.4.14.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_III Dipeptidyl-peptidase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.4 3.4.14.4] </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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [http://pdbe.org/5e33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [http://www.ebi.ac.uk/pdbsum/5e33 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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [http://pdbe.org/5e33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [http://www.ebi.ac.uk/pdbsum/5e33 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5e33 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5e33" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5e33" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dipeptidyl peptidase\|Dipeptidyl peptidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:25, 12 May 2016

OCA — Thu, 12 May 2016 11:25:32 GMT

←Older revision		Revision as of 11:25, 12 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5e33 is ~~ON HOLD until Paper~~ Publication	+	==Structure of human DPP3 in complex with met-enkephalin==
		+	<StructureSection load='5e33' size='340' side='right' caption='[[5e33]], [[Resolution\|resolution]] 1.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5e33]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5E33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5E33 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fvy\|3fvy]], [[3t6b\|3t6b]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dipeptidyl-peptidase_III Dipeptidyl-peptidase III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.14.4 3.4.14.4] </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=5e33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5e33 OCA], [http://pdbe.org/5e33 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5e33 RCSB], [http://www.ebi.ac.uk/pdbsum/5e33 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPP3_HUMAN DPP3_HUMAN]] Cleaves Arg-Arg-beta-naphthylamide.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or "slow" substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors.

-	~~Authors: Kumar~~, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T~~., Wallner, S.~~, Macheroux, P., Gruber, K.	+	Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition.,Kumar P, Reithofer V, Reisinger M, Wallner S, Pavkov-Keller T, Macheroux P, Gruber K Sci Rep. 2016 Mar 30;6:23787. doi: 10.1038/srep23787. PMID:27025154<ref>PMID:27025154</ref>

-	~~Description: Structure~~ of ~~human DPP3 in complex with met~~-~~enkephalin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Wallner~~, S]]	+	<div class="pdbe-citations 5e33" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dipeptidyl-peptidase III]]
		+	[[Category: Gruber, K]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
		+	[[Category: Macheroux, P]]
	[[Category: Pavkov-Keller, T]]		[[Category: Pavkov-Keller, T]]
-	[[Category: Gruber, K]]
	[[Category: Reisinger, M]]		[[Category: Reisinger, M]]
	[[Category: Reithofer, V]]		[[Category: Reithofer, V]]
-	[[Category: ~~Macheroux~~, P]]	+	[[Category: Wallner, S]]
		+	[[Category: Complex]]
		+	[[Category: Hydrolase]]
		+	[[Category: Opioid-peptide]]
		+	[[Category: Peptidase]]
		+	[[Category: Zinc-hydrolase]]

OCA at 11:36, 16 December 2015

OCA — Wed, 16 Dec 2015 11:36:16 GMT

←Older revision		Revision as of 11:36, 16 December 2015
Line 9:		Line 9:
	[[Category: Wallner, S]]		[[Category: Wallner, S]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
-	[[Category: Macheroux, P]]
	[[Category: Pavkov-Keller, T]]		[[Category: Pavkov-Keller, T]]
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
	[[Category: Reisinger, M]]		[[Category: Reisinger, M]]
	[[Category: Reithofer, V]]		[[Category: Reithofer, V]]
		+	[[Category: Macheroux, P]]

OCA at 02:22, 1 December 2015

OCA — Tue, 01 Dec 2015 02:22:35 GMT

←Older revision		Revision as of 02:22, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5e33 is ON HOLD	+	The entry 5e33 is ON HOLD until Paper Publication

	Authors: Kumar, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T., Wallner, S., Macheroux, P., Gruber, K.		Authors: Kumar, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T., Wallner, S., Macheroux, P., Gruber, K.

OCA: Protected "5e33" [edit=sysop:move=sysop]

OCA — Wed, 07 Oct 2015 12:54:14 GMT

Protected "5e33" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:54, 7 October 2015

OCA: New page: '''Unreleased structure''' The entry 5e33 is ON HOLD Authors: Kumar, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T., Wallner, S., Macheroux, P., Gruber, K. Description: Structure ...

OCA — Wed, 07 Oct 2015 12:54:13 GMT

New page: '''Unreleased structure''' The entry 5e33 is ON HOLD Authors: Kumar, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T., Wallner, S., Macheroux, P., Gruber, K. Description: Structure ...

New page

'''Unreleased structure'''

The entry 5e33 is ON HOLD

Authors: Kumar, P., Reithofer, V., Reisinger, M., Pavkov-Keller, T., Wallner, S., Macheroux, P., Gruber, K.

Description: Structure of human DPP3 in complex with met-enkephalin
[[Category: Unreleased Structures]]
[[Category: Wallner, S]]
[[Category: Kumar, P]]
[[Category: Macheroux, P]]
[[Category: Pavkov-Keller, T]]
[[Category: Gruber, K]]
[[Category: Reisinger, M]]
[[Category: Reithofer, V]]