TrkA ECD complex with designed miniprotein ligand

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Design of protein-binding proteins from the target structure alone.

Cao, L.Coventry, B.Goreshnik, I.Huang, B.Sheffler, W.Park, J.S.Jude, K.M.Markovic, I.Kadam, R.U.Verschueren, K.H.G.Verstraete, K.Walsh, S.T.R.Bennett, N.Phal, A.Yang, A.Kozodoy, L.DeWitt, M.Picton, L.Miller, L.Strauch, E.M.DeBouver, N.D.Pires, A.Bera, A.K.Halabiya, S.Hammerson, B.Yang, W.Bernard, S.Stewart, L.Wilson, I.A.Ruohola-Baker, H.Schlessinger, J.Lee, S.Savvides, S.N.Garcia, K.C.Baker, D.

(2022) Nature 605: 551-560

  • DOI: https://doi.org/10.1038/s41586-022-04654-9
  • Primary Citation of Related Structures:  
    7N1J, 7N1K, 7N3T, 7OPB, 7RDH, 7S5B

  • PubMed Abstract: 

    The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge 1-5 . Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.

  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor
A, B
359Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
PHAROS:  P04629
GTEx:  ENSG00000198400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Sequence Annotations
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Designed TrkA-binding miniprotein
C, D
81synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence


Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
DA [auth B]
EA [auth B]
G [auth A]
GA [auth B]
AA [auth B],
DA [auth B],
EA [auth B],
G [auth A],
GA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
IA [auth B]
JA [auth B]
KA [auth B]
LA [auth B]
MA [auth B]
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
FA [auth B]
HA [auth B]
L [auth A]
BA [auth B],
CA [auth B],
FA [auth B],
HA [auth B],
L [auth A],
M [auth A],
N [auth A],
P [auth A],
Q [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.203α = 90
b = 205.695β = 106.422
c = 72.569γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description