8VEI
De novo designed colic acid binder CHD_r1
Summary for 8VEI
| Entry DOI | 10.2210/pdb8vei/pdb |
| Descriptor | CHD_r1 (2 entities in total) |
| Functional Keywords | de novo designed protein, small molecule binder, colic acid, de novo protein |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 14795.93 |
| Authors | Bera, A.K.,An, L.,Baker, D. (deposition date: 2023-12-19, release date: 2024-07-17, Last modification date: 2024-07-31) |
| Primary citation | An, L.,Said, M.,Tran, L.,Majumder, S.,Goreshnik, I.,Lee, G.R.,Juergens, D.,Dauparas, J.,Anishchenko, I.,Coventry, B.,Bera, A.K.,Kang, A.,Levine, P.M.,Alvarez, V.,Pillai, A.,Norn, C.,Feldman, D.,Zorine, D.,Hicks, D.R.,Li, X.,Sanchez, M.G.,Vafeados, D.K.,Salveson, P.J.,Vorobieva, A.A.,Baker, D. Binding and sensing diverse small molecules using shape-complementary pseudocycles. Science, 385:276-282, 2024 Cited by PubMed Abstract: We describe an approach for designing high-affinity small molecule-binding proteins poised for downstream sensing. We use deep learning-generated pseudocycles with repeating structural units surrounding central binding pockets with widely varying shapes that depend on the geometry and number of the repeat units. We dock small molecules of interest into the most shape complementary of these pseudocycles, design the interaction surfaces for high binding affinity, and experimentally screen to identify designs with the highest affinity. We obtain binders to four diverse molecules, including the polar and flexible methotrexate and thyroxine. Taking advantage of the modular repeat structure and central binding pockets, we construct chemically induced dimerization systems and low-noise nanopore sensors by splitting designs into domains that reassemble upon ligand addition. PubMed: 39024436DOI: 10.1126/science.adn3780 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.03 Å) |
Structure validation
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