9B25 | pdb_00009b25

Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with NA98

• PDB DOI: https://doi.org/10.2210/pdb9B25/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-03-14 Released: 2025-08-27 
• Deposition Author(s): Nwachukwu, J.C., Min, C.K., Papa, A., Rangarajan, E.S., Izard, T., Sharma, A., Nettles, K.W.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with NA98

Nwachukwu, J.C., Min, C.K., Papa, A., Rangarajan, E.S., Izard, T., Sharma, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.15 kDa 
• Atom Count: 8,471 
• Modeled Residue Count: 969 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B, C, D	251	Homo sapiens	Mutation(s): 2  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AIZ (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(1r,4r)-N-[4-(4-{[6-hydroxy-2-(4-hydroxyphenyl)-1-benzothiophen-3-yl]oxy}phenoxy)butyl]-4-(trifluoromethyl)cyclohexane-1-carboxamide C32 H32 F3 N O5 S MVWQFGVVPQWODY-HZCBDIJESA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A, B, C, D	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.829	α = 90
b = 199.98	β = 119.07
c = 55.246	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Nwachukwu, J.C., Min, C.K., Papa, A., Rangarajan, E.S., Izard, T., Sharma, A., Nettles, K.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release