7L33

X-ray Structure of a Cu-Bound De Novo Designed Peptide Trimer

• PDB DOI: https://doi.org/10.2210/pdb7L33/pdb

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


• Deposited: 2020-12-17 Released: 2021-08-11 
• Deposition Author(s): Chakraborty, S., Wawrzak, Z., Prasad, P., Mitra, S., Prakash, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.294 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 

Literature

De Novo Design of a Self-Assembled Artificial Copper Peptide that Activates and Reduces Peroxide

Mitra, S., Prakash, D., Rajabimoghadam, K., Wawrzak, Z., Prasad, P., Wu, T., Misra, S.K., Sharp, J.S., Garcia-Bosch, I., Chakraborty, S.

(2021) ACS Catal 11: 10267-10278

• DOI: https://doi.org/10.1021/acscatal.1c02132

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.97 kDa 
• Atom Count: 702 
• Modelled Residue Count: 95 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cu-3SCC	A, B, C	32	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.294 
• R-Value Work: 0.269 
• R-Value Observed: 0.270 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.26	α = 90
b = 39.26	β = 90
c = 83.63	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Chakraborty, S., Wawrzak, Z., Prasad, P., Mitra, S., Prakash, D.

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description