9PPU | pdb_00009ppu

Beta-sandwich forming metallopeptide

• PDB DOI: https://doi.org/10.2210/pdb9PPU/pdb

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


• Deposited: 2025-07-21 Released: 2026-04-22 
• Deposition Author(s): Dang, V.T., Nguyen, A.I.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

A bis-macrocylic peptide ligand mimicking the beta-sandwich active site of multicopper oxidases.

Dang, V.T., Drena, A., Telser, J., Wofford, L., Nguyen, A.I.

(2026) Dalton Trans 55: 5877-5881

• PubMed: 41969027 
• DOI: https://doi.org/10.1039/d6dt00494f
• Primary Citation Related Structures: 
  9PPU


• PubMed Abstract: 
  

  The active site of multicopper oxidases contains three Cu ions coordinated to a β-sandwich motif. Here, we designed a small peptide ligand that closely mimics the β-sandwich. We verified the sandwich architecture by X-ray crystallography, showing its high resemblance to the active site and ability to coordinate two Cu(II) ions.

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Organizational Affiliation: 
• Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA. [e-mail].
Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
College of Science, Health, and Pharmacy, Roosevelt University, Chicago, IL 60605, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content 

• Total Structure Weight: 3.55 kDa 
• Atom Count: 288 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed metallopeptide	A [auth B]	12	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed metallopeptide	B [auth A]	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACA (Subject of Investigation/LOI)	E [auth B]	6-AMINOHEXANOIC ACID C6 H13 N O2 SLXKOJJOQWFEFD-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	C [auth B], F [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
FMT	D [auth B], G [auth A], H [auth A], I [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN	A [auth B]	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.32	α = 90
b = 41.32	β = 90
c = 53.493	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Dang, V.T., Nguyen, A.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM154793-01

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Database references