8hdv | pdb_00008hdv

De novo design cavitated protein without predefined topology

spinqualitylabelsall models 8hdv, resolution 2.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8hdv is a 2 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.65Å Ligands: MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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