9N06 | pdb_00009n06

Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol A

PDB DOI: https://doi.org/10.2210/pdb9N06/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Melanotaenia fluviatilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-23 Released: 2026-01-28
Deposition Author(s): Pederick, J.L., Bruning, J.B.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.197 (Depositor), 0.164 (DCC)
R-Value Work:
0.165 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol A

Pederick, J.L., McDougal, D.P., Shearwin-Whyatt, L., Woolman, J.C., Grutzner, F., Bruning, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 57.98 kDa
Atom Count: 3,938
Modeled Residue Count: 480
Deposited Residue Count: 502
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	251	Melanotaenia fluviatilis	Mutation(s): 0 Gene Names: ESR1
UniProt
Find proteins for D6N7U3 (Melanotaenia fluviatilis) Explore D6N7U3 Go to UniProtKB: D6N7U3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D6N7U3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2OH (Subject of Investigation/LOI) Query on 2OH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	4,4'-PROPANE-2,2-DIYLDIPHENOL C₁₅ H₁₆ O₂ IISBACLAFKSPIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.197 (Depositor), 0.164 (DCC)
R-Value Work: 0.165 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.569	α = 90
b = 111.569	β = 90
c = 99.255	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP230100609

Revision History (Full details and data files)

Version 1.0: 2026-01-28
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.