6w3f: Difference between revisions

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<StructureSection load='6w3f' size='340' side='right'caption='[[6w3f]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
<StructureSection load='6w3f' size='340' side='right'caption='[[6w3f]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6w3f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W3F FirstGlance]. <br>
<table><tr><td colspan='2'>[[6w3f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W3F 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=6w3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w3f OCA], [https://pdbe.org/6w3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w3f RCSB], [https://www.ebi.ac.uk/pdbsum/6w3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w3f ProSAT]</span></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]] 1.83&#8491;</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=6w3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w3f OCA], [https://pdbe.org/6w3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w3f RCSB], [https://www.ebi.ac.uk/pdbsum/6w3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w3f ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
An enumerative algorithm for de novo design of proteins with diverse pocket structures.,Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D Proc Natl Acad Sci U S A. 2020 Aug 24. pii: 2005412117. doi:, 10.1073/pnas.2005412117. PMID:32839327<ref>PMID:32839327</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6w3f" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Synthetic construct sequences]]
[[Category: Synthetic construct]]
[[Category: Baker, D]]
[[Category: Baker D]]
[[Category: Basanta, B]]
[[Category: Basanta B]]
[[Category: Bick, M J]]
[[Category: Bick MJ]]
[[Category: Sankaran, B]]
[[Category: Sankaran B]]
[[Category: Biosynthetic protein]]
[[Category: Ntf2-like]]
[[Category: Synthetic]]
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