OCA at 05:23, 9 August 2023

2023-08-09T05:23:21Z

←Older revision		Revision as of 05:23, 9 August 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8b1i is ~~ON HOLD until Paper~~ Publication	+	==DtpB-Nb132-MS==
		+	<StructureSection load='8b1i' size='340' side='right'caption='[[8b1i]], [[Resolution\|resolution]] 2.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8b1i]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8B1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B1I FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=8b1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b1i OCA], [https://pdbe.org/8b1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b1i RCSB], [https://www.ebi.ac.uk/pdbsum/8b1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b1i ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DTPB_ECOLI DTPB_ECOLI] Proton-dependent permease that transports di- and tripeptides. Has a clear preference for dipeptides and tripeptides composed of L-amino acids, and discriminates dipeptides on the basis of the position of charges within the substrate.<ref>PMID:18485005</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proton-dependent oligopeptide transporters (POTs) are promiscuous transporters of the major facilitator superfamily that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several POT homologs have been studied extensively at the structural and molecular level. However, the molecular basis of recognition and transport of diverse peptide substrates has remained elusive. We present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe whether all 8400 natural di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides with compact hydrophobic residues are the best DtpB binders.

-	~~Authors~~:	+	Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition.,Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm AS, Cornaciu I, Marquez JA, Pardon E, Steyaert J, Low C Cell Rep. 2023 Jul 18;42(8):112831. doi: 10.1016/j.celrep.2023.112831. PMID:37467108<ref>PMID:37467108</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8b1i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Lama glama]]
		+	[[Category: Large Structures]]
		+	[[Category: Bartels K]]
		+	[[Category: Cornaciu I]]
		+	[[Category: Dupeux F]]
		+	[[Category: Finocchio G]]
		+	[[Category: Humm AS]]
		+	[[Category: Jungnickel K]]
		+	[[Category: Killer M]]
		+	[[Category: Kotov V]]
		+	[[Category: Lei J]]
		+	[[Category: Loew C]]
		+	[[Category: Marquez J]]
		+	[[Category: Pardon E]]
		+	[[Category: Steinke J]]
		+	[[Category: Steyeart J]]
		+	[[Category: Strauss J]]

OCA at 16:44, 19 October 2022

2022-10-19T16:44:19Z

←Older revision		Revision as of 16:44, 19 October 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8b1i is ON HOLD	+	The entry 8b1i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8b1i" [edit=sysop:move=sysop]

2022-09-21T06:29:41Z

Protected "8b1i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:29, 21 September 2022

OCA: New page: '''Unreleased structure''' The entry 8b1i is ON HOLD Authors: Description: Category: Unreleased Structures

2022-09-21T06:29:40Z

New page: '''Unreleased structure''' The entry 8b1i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8b1i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

8b1i - Revision history

OCA at 05:23, 9 August 2023

OCA at 16:44, 19 October 2022

OCA: Protected "8b1i" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8b1i is ON HOLD Authors: Description: Category: Unreleased Structures