6W3D
Rd1NTF2_05 with long sheet
Summary for 6W3D
| Entry DOI | 10.2210/pdb6w3d/pdb |
| Descriptor | Rd1NTF2_05 (2 entities in total) |
| Functional Keywords | ntf2-like, synthetic, biosynthetic protein |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 15705.79 |
| Authors | Bick, M.J.,Basanta, B.,Sankaran, B.,Baker, D. (deposition date: 2020-03-09, release date: 2020-04-15, Last modification date: 2024-04-03) |
| Primary citation | Basanta, B.,Bick, M.J.,Bera, A.K.,Norn, C.,Chow, C.M.,Carter, L.P.,Goreshnik, I.,Dimaio, F.,Baker, D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proc.Natl.Acad.Sci.USA, 117:22135-22145, 2020 Cited by PubMed Abstract: To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins. PubMed: 32839327DOI: 10.1073/pnas.2005412117 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.38 Å) |
Structure validation
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