9NKO
Coevolved affibody pair A3B3
Summary for 9NKO
| Entry DOI | 10.2210/pdb9nko/pdb |
| Related | 9NKM 9NKN |
| Descriptor | A3 affibody, B3 affibody (3 entities in total) |
| Functional Keywords | coevolution, complex, affibody, protein binding |
| Biological source | synthetic construct More |
| Total number of polymer chains | 4 |
| Total formula weight | 31158.97 |
| Authors | Jude, K.M.,Yang, A.,Garcia, K.C. (deposition date: 2025-03-01, release date: 2026-02-04, Last modification date: 2026-02-25) |
| Primary citation | Yang, A.,Jiang, H.,Jude, K.M.,Akpinaroglu, D.,Allenspach, S.,Li, A.J.,Bowden, J.,Perez, C.P.,Liu, L.,Huang, P.S.,Kortemme, T.,Listgarten, J.,Garcia, K.C. Structural ontogeny of protein-protein interactions. Science, 391:eadx6931-eadx6931, 2026 Cited by PubMed Abstract: Understanding how protein binding sites evolve interactions with other proteins could hold clues to targeting "undruggable" surfaces. We used synthetic coevolution to engineer new interactions between naïve surfaces, simulating the de novo formation of protein complexes. We isolated seven distinct structural families of protein Z-domain complexes and found that synthetic complexes explore multiple shallow energy wells through ratchet-like docking modes, whereas complexes formed by natural binding sites converged in a deep energy well with a relatively fixed geometry. Epistasis analysis of a machine learning-estimated fitness landscape revealed "seed" contacts between binding partners that anchored the earliest stages of encounter complex formation. Our results suggest that "silent" surfaces have a shallower energy landscape than natural binding sites, disfavoring tight binding, likely owing to evolutionary counterselection. PubMed: 41678610DOI: 10.1126/science.adx6931 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.72 Å) |
Structure validation
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