9NKN | pdb_00009nkn

Coevolved affibody pair A2B2

• PDB DOI: https://doi.org/10.2210/pdb9NKN/pdb

• Classification: PROTEIN BINDING
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-01 Released: 2026-02-04 
• Deposition Author(s): Jude, K.M., Yang, A., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Models: experimental

Literature

Structural ontogeny of protein-protein interactions.

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.

(2026) Science 391: eadx6931-eadx6931

• PubMed: 41678610 
• DOI: https://doi.org/10.1126/science.adx6931
• Primary Citation Related Structures: 
  9NKM, 9NKN, 9NKO, 9NKP, 9NKQ, 9NKR, 9NKS


• 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.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.62 kDa 
• Atom Count: 891 
• Modeled Residue Count: 110 
• Deposited Residue Count: 136 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A2 affibody	A	68	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B2 affibody	B	68	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/1170

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.655	α = 90
b = 73.392	β = 90
c = 39.572	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Jude, K.M., Yang, A., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM150125
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release
  
• Version 1.1: 2026-02-25
  Changes: Database references