5tvy

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Current revision (14:23, 6 March 2024) (edit) (undo)
 
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<StructureSection load='5tvy' size='340' side='right'caption='[[5tvy]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
<StructureSection load='5tvy' size='340' side='right'caption='[[5tvy]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5tvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TVY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5tvy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TVY FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XPE:3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL'>XPE</scene></td></tr>
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</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&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5tvv|5tvv]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XPE:3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL'>XPE</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xynA, BSU18840 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tvy OCA], [https://pdbe.org/5tvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tvy RCSB], [https://www.ebi.ac.uk/pdbsum/5tvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tvy ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
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<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=5tvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tvy OCA], [http://pdbe.org/5tvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tvy RCSB], [http://www.ebi.ac.uk/pdbsum/5tvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tvy ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/XYNA_BACSU XYNA_BACSU]
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We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.
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Computational design of environmental sensors for the potent opioid fentanyl.,Bick MJ, Greisen PJ, Morey KJ, Antunes MS, La D, Sankaran B, Reymond L, Johnsson K, Medford JI, Baker D Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909. PMID:28925919<ref>PMID:28925919</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5tvy" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacsu]]
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[[Category: Bacillus subtilis subsp. subtilis str. 168]]
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[[Category: Endo-1,4-beta-xylanase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Antunes, M S]]
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[[Category: Antunes MS]]
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[[Category: Baker, D]]
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[[Category: Baker D]]
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[[Category: Bick, M J]]
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[[Category: Bick MJ]]
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[[Category: Greisen, P J]]
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[[Category: Greisen PJ]]
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[[Category: Johnsson, K]]
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[[Category: Johnsson K]]
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[[Category: La, D]]
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[[Category: La D]]
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[[Category: Medford, J I]]
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[[Category: Medford JI]]
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[[Category: Morey, K J]]
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[[Category: Morey KJ]]
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[[Category: Reymond, L]]
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[[Category: Reymond L]]
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[[Category: Sankaran, B]]
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[[Category: Sankaran B]]
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[[Category: Computational design]]
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[[Category: Fentanyl]]
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[[Category: Hydrolase]]
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Current revision

Computationally Designed Fentanyl Binder - Fen49

PDB ID 5tvy

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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