View source for 8b1f


==DtpB-Nb132-AV==
<StructureSection load='8b1f' size='340' side='right'caption='[[8b1f]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8b1f]] 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=8B1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8B1F 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]] 2.35&#8491;</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=8b1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8b1f OCA], [https://pdbe.org/8b1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8b1f RCSB], [https://www.ebi.ac.uk/pdbsum/8b1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8b1f ProSAT]</span></td></tr>
</table>
<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.

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 Aug 29;42(8):112831. doi: 10.1016/j.celrep.2023.112831. Epub 2023 , Jul 18. PMID:37467108<ref>PMID:37467108</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8b1f" 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]]