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)

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
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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AIZ (Subject of Investigation/LOI) Query on A1AIZ Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM Query on 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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-27

Deposition Author(s):

Nwachukwu, J.C.

Rangarajan, E.S.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.