9DED | pdb_00009ded

Designed protein n8

• PDB DOI: https://doi.org/10.2210/pdb9DED/pdb

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


• Deposited: 2024-08-28 Released: 2025-02-19 
• Deposition Author(s): Pellock, S.J., Lauko, A., Bera, A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Defense Advanced Research Projects Agency (DARPA), Defense Threat Reduction Agency (DTRA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Computational design of serine hydrolases.

Lauko, A., Pellock, S.J., Sumida, K.H., Anishchenko, I., Juergens, D., Ahern, W., Jeung, J., Shida, A.F., Hunt, A., Kalvet, I., Norn, C., Humphreys, I.R., Jamieson, C., Krishna, R., Kipnis, Y., Kang, A., Brackenbrough, E., Bera, A.K., Sankaran, B., Houk, K.N., Baker, D.

(2025) Science 388: eadu2454-eadu2454

• PubMed: 39946508 
• DOI: https://doi.org/10.1126/science.adu2454
• Primary Citation Related Structures: 
  9DED, 9DEE, 9DEF, 9DEG, 9DEH, 9MRB


• PubMed Abstract: 
  

  The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation method for assessing active site preorganization at each step in the reaction to design enzymes starting from minimal active site descriptions. Experimental characterization revealed catalytic efficiencies ( k _cat / K _m ) up to 2.2 × 10 ⁵ M ^-1 s ^-1 and crystal structures that closely match the design models (Cα root mean square deviations <1 angstrom). Selection for structural compatibility across the reaction coordinate enabled identification of new catalysts remove with five different folds distinct from those of natural serine hydrolases. Our de novo approach provides insight into the geometric basis of catalysis and a roadmap for designing enzymes that catalyze multistep transformations.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.
Department of Chemistry, University of Washington, Seattle, WA, USA.
Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA.
Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
Medical Scientist Training Program, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.69 kDa 
• Atom Count: 1,041 
• Modeled Residue Count: 114 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Design protein n8	A	116	synthetic construct	Mutation(s): 0  Gene Names: AX245_05475, DX05_04210, EN72_04240, RDF_0711, SA111_00802, TH70_0496, WA02_00660, WA04_01435, WA05_01900, WA34_15420

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.556	α = 90
b = 31.558	β = 101.322
c = 40.794	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Pellock, S.J., Lauko, A., Bera, A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
Other private		--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--
Defense Advanced Research Projects Agency (DARPA)	United States	--
Defense Threat Reduction Agency (DTRA)	United States	--

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Database references
• Version 1.2: 2025-04-30
  Changes: Database references