9OXQ | pdb_00009oxq

X-ray crystal structure of Beta-Barrel forming peptide macrocycle

• PDB DOI: https://doi.org/10.2210/pdb9OXQ/pdb

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


• Deposited: 2025-06-04 Released: 2025-06-18 
• Deposition Author(s): Dang, V.T., Nguyen, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

beta-barrels from short macrocyclic peptides.

Dang, V.T., Martynowycz, M.W., McElheny, D., Nguyen, A.I.

(2026) Chem Commun (Camb) 62: 2304-2308

• PubMed: 41489626 
• DOI: https://doi.org/10.1039/d5cc06640a
• Primary Citation Related Structures: 
  9OXP, 9OXQ, 9Q63, 9Q6E


• PubMed Abstract: 
  

  β-Barrels are ubiquitous motifs in protein structures, but the fundamental rules underlying their formation are unclear, and their de novo design remains highly challenging. Small peptides that form barrels are especially scarce. Here, we report barrels with the shortest staves (6 residues, ∼60% of previous record) and smallest shear number ( S = 4) so far, formed from 12-residue macrocyclic peptides. The miniature barrel has anomalous structural features, demonstrated by solution phase and crystallographic characterization; there is a pronounced and essential backbone kink imparted by an achiral residue, N -methylglycine, as well as four structural water molecules stitching the seams of the barrel. These results provide insights into how extremely short sequences could form barrel assemblies.

---

Organizational Affiliation: 
• Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA. [e-mail].
Hauptman-Woodward Medical Research Institute, University at Buffalo, Buffalo, New York, 14203, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR relaxation study

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.98 kDa 
• Atom Count: 1,030 
• Modeled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MC4H (ORN)WFHSH(ORN)FIH(SAR)H peptide macrocycle	A, C, E, G	12	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MC4H (ORN)FIH(SAR)H(ORN)WFHSH peptide macrocycle	B, D, F, H	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth C], K [auth C], L [auth E], M [auth G], N [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN	A, C, E, G	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
SAR	A, C, E, G	PEPTIDE LINKING	C3 H7 N O2		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.012	α = 90
b = 40.715	β = 103.41
c = 46.939	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: 2025-06-18 
Deposition Author(s): Dang, V.T., Nguyen, A.

---

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: 2025-06-18
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Structure summary
• Version 1.2: 2026-01-14
  Changes: Database references
• Version 1.3: 2026-02-11
  Changes: Database references