View source for 8hdv


==De novo design cavitated protein without predefined topology==
<StructureSection load='8hdv' size='340' side='right'caption='[[8hdv]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8hdv]] 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=8HDV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8HDV 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]] 2.65&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=8hdv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8hdv OCA], [https://pdbe.org/8hdv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8hdv RCSB], [https://www.ebi.ac.uk/pdbsum/8hdv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8hdv ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones without predefined architectures by introducing tailored restraints into the backbone sampling driven by SCUBA (Side Chain-Unknown Backbone Arrangement), a neural network statistical energy function. For 521 out of 5816 designs, the root-mean-square deviations (RMSDs) of the Calpha atoms for the AlphaFold2-predicted structures and our designed structures are within 2.0 A. We experimentally tested 10 designed proteins and determined the crystal structures of two of them. One closely agrees with the designed model, while the other forms a domain-swapped dimer, where the partial structures are in agreement with the designed structures. Our results indicate that data-driven methods such as SCUBA hold great potential for designing de novo proteins with tailored small-molecule-binding function.

De novo design of cavity-containing proteins with a backbone-centered neural network energy function.,Xu Y, Hu X, Wang C, Liu Y, Chen Q, Liu H Structure. 2024 Apr 4;32(4):424-432.e4. doi: 10.1016/j.str.2024.01.006. Epub 2024 , Feb 6. PMID:38325370<ref>PMID:38325370</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8hdv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Hu X]]
[[Category: Xu Y]]