7a8s
From Proteopedia
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==de novo designed ba8-barrel sTIM11 with an alpha-helical extension== | ==de novo designed ba8-barrel sTIM11 with an alpha-helical extension== | ||
| - | <StructureSection load='7a8s' size='340' side='right'caption='[[7a8s]]' scene=''> | + | <StructureSection load='7a8s' size='340' side='right'caption='[[7a8s]], [[Resolution|resolution]] 1.58Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7A8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7A8S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7a8s]] is a 1 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=7A8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7A8S 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=7a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7a8s OCA], [https://pdbe.org/7a8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7a8s RCSB], [https://www.ebi.ac.uk/pdbsum/7a8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7a8s 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]] 1.58Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=7a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7a8s OCA], [https://pdbe.org/7a8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7a8s RCSB], [https://www.ebi.ac.uk/pdbsum/7a8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7a8s ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The ability to construct novel enzymes is a major aim in de novo protein design. A popular enzyme fold for design attempts is the TIM barrel. This fold is a common topology for enzymes and can harbor many diverse reactions. The recent de novo design of a four-fold symmetric TIM barrel provides a well understood minimal scaffold for potential enzyme designs. Here we explore opportunities to extend and diversify this scaffold by adding a short de novo helix on top of the barrel. Due to the size of the protein, we developed a design pipeline based on computational ab initio folding that solves a less complex sub-problem focused around the helix and its vicinity and adapt it to the entire protein. We provide biochemical characterization and a high-resolution X-ray structure for one variant and compare it to our design model. The successful extension of this robust TIM-barrel scaffold opens opportunities to diversify it towards more pocket like arrangements and as such can be considered a building block for future design of binding or catalytic sites. | ||
| + | |||
| + | Extension of a de novo TIM barrel with a rationally designed secondary structure element.,Wiese JG, Shanmugaratnam S, Hocker B Protein Sci. 2021 Mar 15. doi: 10.1002/pro.4064. PMID:33723882<ref>PMID:33723882</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7a8s" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Synthetic construct]] | ||
[[Category: Hocker B]] | [[Category: Hocker B]] | ||
[[Category: Shanmugaratnam S]] | [[Category: Shanmugaratnam S]] | ||
[[Category: Wiese JG]] | [[Category: Wiese JG]] | ||
Current revision
de novo designed ba8-barrel sTIM11 with an alpha-helical extension
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