12YG | pdb_000012yg

HelloB-GGFFAA-A6Dpp - de novo peptide with tertiary structure

• PDB DOI: https://doi.org/10.2210/pdb12YG/pdb

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


• Deposited: 2026-04-22 Released: 2026-10-28 
• Deposition Author(s): Ganatra, P.
• Funding Organization(s): Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Porous Framework Assembly Creates Functional Tertiary Folds in Small Peptides

Ganatra, P., Wang, D.F., Nichols, S., Dang, V.T., Brunzelle, J.S., Jana, P., Nguyen, A.I.

(2026) J Am Chem Soc 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1.91 kDa 
• Atom Count: 194 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HelloB-GGFFAA-A6Dpp- de novo peptide with tertiary structure	A	19	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA (Subject of Investigation/LOI)	B [auth A]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
AIB	A	ALA	Methylation	C4 H9 N O2
DPP	A	ALA	Amination	C3 H8 N2 O2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.785	α = 90
b = 9.278	β = 112.1
c = 38.829	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Ganatra, P.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357
National Science Foundation (NSF, United States)	United States	2440121
Department of Energy (DOE, United States)	United States	DOE DE-SC0025651

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release