9BQR | pdb_00009bqr

X-ray Structure of a Second-Sphere H-bond Deletion Mutant of a De Novo Designed Self Assembled Peptide Tetramer Featuring a Cu(His)4(H2O) Coordination Motif

• PDB DOI: https://doi.org/10.2210/pdb9BQR/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-05-10 Released: 2025-04-16 
• Deposition Author(s): Chakraborty, S., Sony, S., Prakash, D., Andi, B.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.236 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Controlling outer-sphere solvent reorganization energy to turn on or off the function of artificial metalloenzymes.

Prakash, D., Mitra, S., Sony, S., Murphy, M., Andi, B., Ashley, L., Prasad, P., Chakraborty, S.

(2025) Nat Commun 16: 3048-3048

• PubMed: 40155633 
• DOI: https://doi.org/10.1038/s41467-025-57904-5
• Primary Citation Related Structures: 
  8VHS, 9BQR


• PubMed Abstract: 
  

  Metalloenzymes play essential roles in biology. However, unraveling how outer-sphere interactions can be predictably controlled to influence their functions remains a significant challenge. Inspired by Cu enzymes, we demonstrate how variations in the primary, secondary, and outer coordination-sphere interactions of de novo designed artificial copper proteins (ArCuPs) within trimeric (3SCC) and tetrameric (4SCC) self-assemblies-featuring a trigonal Cu(His) ₃ and a square pyramidal Cu(His) ₄ (OH ₂ ) coordination-influence their catalytic and electron transfer properties. While 3SCC electrocatalyzes C-H oxidation, 4SCC does not. Cu ^I -3SCC reacts more rapidly with H ₂ O ₂ than O ₂ , whereas 4SCC is less active. Electron transfer, reorganization energies, and extended H ₂ O-mediated hydrogen bonding patterns provide insights into the observed reactivity differences. The inactivity of 4SCC is attributed to a significant solvent reorganization energy barrier mediated by a specific His---Glu hydrogen bond. When this hydrogen bond is disrupted, the solvent reorganization energy is reduced, and C-H peroxidation activity is restored.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA.
Northwestern University, Evanston, IL, USA.
Weill Cornell Medicine, New York, NY, USA.
Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA.
Regeneron Pharmaceuticals, Tarrytown, NY, USA.
Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 16.12 kDa 
• Atom Count: 1,233 
• Modeled Residue Count: 152 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
K6E/E8K Double Mutant of Cu-4SCC	A, B, C, D	39	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU (Subject of Investigation/LOI)	E [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.236 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.553	α = 90
b = 45.309	β = 98.54
c = 40.524	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Chakraborty, S., Sony, S., Prakash, D., Andi, B.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release