11SE | pdb_000011se

Covalent stabilizer compound 8 for the interaction between 14-3-3 sigma and Estrogen receptor-alpha peptide

• PDB DOI: https://doi.org/10.2210/pdb11SE/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-03-11 Released: 2026-08-26 
• Deposition Author(s): Knapp, M.S., Tang, J.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.256 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Covalent stabilizers of the interaction between 14-3-3 and Estrogen receptor-alpha

Rama, J., Skepper, C.K.

To be published.

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 - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.77 kDa 
• Atom Count: 3,896 
• Modeled Residue Count: 466 
• Deposited Residue Count: 526 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A, B [auth C]	248	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	C [auth X], D [auth Y]	15	Homo sapiens	Mutation(s): 0  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1DAD( Subject of Investigation/LOI)	E [auth A]	3-chloro-5-{[(1S)-1-methoxy-1-methyl-3-oxo-1,3-dihydro-2-benzofuran-4-yl]oxy}-4H-1,2,6-thiadiazin-4-one C13 H9 Cl N2 O5 S RQJUWVIMZLHWNC-ZDUSSCGKSA-N
A1DAE( Subject of Investigation/LOI)	F [auth C]	3-chloro-5-{[(1R)-1-methoxy-1-methyl-3-oxo-1,3-dihydro-2-benzofuran-4-yl]oxy}-4H-1,2,6-thiadiazin-4-one C13 H9 Cl N2 O5 S RQJUWVIMZLHWNC-CYBMUJFWSA-N
MG	G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	C [auth X], D [auth Y]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.256 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.051	α = 90
b = 136.476	β = 90
c = 163.101	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-26 
Deposition Author(s): Knapp, M.S., Tang, J.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-08-26
  Type: Initial release