7rmy | pdb_00007rmy

De Novo designed tunable protein pockets, D_3-337

spinqualitylabelsall models 7rmy, resolution 3.17Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7rmy is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds. De novo design of protein homodimers containing tunable symmetric protein pockets.,Hicks DR, Kennedy MA, Thompson KA, DeWitt M, Coventry B, Kang A, Bera AK, Brunette TJ, Sankaran B, Stoddard B, Baker D Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2113400119. doi:, 10.1073/pnas.2113400119. Epub 2022 Jul 21. PMID:35862457 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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