6naf: Difference between revisions
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New page: '''Unreleased structure''' The entry 6naf is ON HOLD Authors: Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D. Description: De novo designed homo-trimeric amantadine-bindi... |
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==De novo designed homo-trimeric amantadine-binding protein== | |||
<StructureSection load='6naf' size='340' side='right'caption='[[6naf]], [[Resolution|resolution]] 1.92Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6naf]] 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=6NAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NAF FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution|Resolution]] 1.923Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=308:(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE'>308</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6naf OCA], [https://pdbe.org/6naf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6naf RCSB], [https://www.ebi.ac.uk/pdbsum/6naf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6naf ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems. | |||
De novo design of a homo-trimeric amantadine-binding protein.,Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D Elife. 2019 Dec 19;8. pii: 47839. doi: 10.7554/eLife.47839. PMID:31854299<ref>PMID:31854299</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Baker | <div class="pdbe-citations 6naf" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Selvaraj | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Baker D]] | |||
[[Category: Cuneo MJ]] | |||
[[Category: Myles DAA]] | |||
[[Category: Park J]] | |||
[[Category: Selvaraj B]] | |||
Latest revision as of 09:15, 25 October 2023
De novo designed homo-trimeric amantadine-binding protein
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