SAXSdb — 9n06

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Estrogen receptor

Melanotaenia fluviatilis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 310–553 Chain B； UniProt 310–553	Not recorded	GOL GLYCEROL × 1 2OH 4,4'-PROPANE-2,2-DIYLDIPHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289.15 K；4% v/v tacsimate pH 5, 12% PEG3350	Resolution 1.90 Å R-free 0.197

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9N06	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9D8Q Crystal structure of Estrogen Receptor alpha from Melanotaenia fluviatilis bound to estradiol and human SRC2 peptide Deposited 2024-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 310–553（244 aa）	Not recorded	EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；9-10% Tacsimate pH 7.0, 22% PEG3000	Resolution 2.75 Å R-free 0.261
9MDV Apo form of the estrogen receptor alpha ligand binding domain of Melanotaenia fluviatilis Deposited 2024-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M NaCl, 0.1 M PIPES pH 7, 22% PEG 2000 MME	Resolution 2.00 Å R-free 0.286
9N03 Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol AF Deposited 2025-01-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	0CZ 4,4'-(1,1,1,3,3,3-hexafluoropropane-2,2-diyl)diphenol × 3 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M sodium malonate pH 4, 12% PEG 3350	Resolution 1.80 Å R-free 0.218
9N0A Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol AP Deposited 2025-01-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	A1BUG 4,4'-(1-phenylethane-1,1-diyl)diphenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；12% PEG 3350, 0.1 M sodium malonate pH 5	Resolution 2.50 Å R-free 0.261
9N0C Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol BPBP Deposited 2025-01-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	A1BVI 4,4'-(diphenylmethylene)diphenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；20% PEG 3350, 0.2 M lithium citrate tribasic dihydrate	Resolution 1.47 Å R-free 0.266
9N24 Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol B Deposited 2025-01-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	H3W bisphenol-B × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M sodium malonate pH 4, 20% PEG 3350	Resolution 2.30 Å R-free 0.261
9N25 Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol Z Deposited 2025-01-27	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	BPZ 4,4'-cyclohexane-1,1-diyldiphenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；4% v/v tacsimate pH 5, 12% PEG3350	Resolution 2.15 Å R-free 0.232
9N27 Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol TMC Deposited 2025-01-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa） Chain B 310–553（244 aa）	Not recorded	A1BVK (2~5~S)-2~3~,2~3~,2~5~-trimethyl-2~3~,2~4~,2~5~,2~6~-tetrahydro-2~2~H-[1~1~,2~1~:2~1~,3~1~-terphenyl]-1~4~,3~4~-diol × 4 A1BWR (2~5~R)-2~3~,2~3~,2~5~-trimethyl-2~3~,2~4~,2~5~,2~6~-tetrahydro-2~2~H-[1~1~,2~1~:2~1~,3~1~-terphenyl]-1~4~,3~4~-diol × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；12% PEG 3350, 0.1 M sodium malonate pH 5	Resolution 2.15 Å R-free 0.277
9N28 Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with estradiol and D22 13mer Deposited 2025-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa）	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.01M iron (III) chloride hexahydrate, 0.1M sodium citrate tribasic dihydrate pH 5.6, 10% Jeffamine M-600	Resolution 2.10 Å R-free 0.268
9N2J Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with estradiol Deposited 2025-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 310–553（244 aa）	Not recorded	EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；10-14% PEG 3350, 0.1 M ammonium citrate tribasic	Resolution 2.90 Å R-free 0.318

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D6N7U3_MELFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–251； UniProt 310–553 Author chain B； PDBConstruct 8–251； UniProt 310–553

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9n06
Deposition date deposition_date	2025-01-23
最后修订 last_revision	2026-01-28
Structure title title	Crystal structure of Melanotaenia fluviatilis estrogen receptor alpha ligand binding domain complexed with Bisphenol A
Keywords keywords	ligand binding domain, transcription factor, endocrine disrupting compound, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.01 Å
Radius of gyration Rg (electron density) rg_electron	21.78 Å
Forward intensity I(0) i0	46018200.00
Molecular weight molecular_weight	54298.0 kDa
Excluded volume excluded_volume	68645 Å³
Envelope volume envelope_volume	78422 Å³
Hydration-shell volume shell_volume	28909 Å³
Envelope diameter envelope_diameter	74.2 Å
Shell Rg shell_rg	29.52 Å
Envelope Rg envelope_rg	21.83 Å
Shape Rg shape_rg	21.78 Å
Total Rg total_rg	22.68 Å
Total atoms total_atoms	3798
Residues n_residues	480
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	68.5 Å
Rg (real space) rg_real	22.83 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	4.6020e+07
I(0) uncertainty (real space) i0_real_error	5.5870e+05
Rg (reciprocal space) rg_reciprocal	22.88 Å
I(0) (reciprocal space) i0_reciprocal	46020000.0000
Solution quality estimate total_estimate	0.8268
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.4 Å
Skewness Skewness skewness	0.069
Kurtosis Kurtosis kurtosis	-0.503
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12310000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Estrogen receptor
Molecular weight formula_weight	28714.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3938

MHHHHHHMPPEQVLILLQGAEPPILCSRQKLSRPYTEVTMMTLLTSMADKELVHMIAWAKKLPGFLQLSLHDQVLLLESSWLEVLMIGLIWRSIHCPGKLIFAQDLILDRNEGDCVEGMTEIFDMLLATASRFRLLKLKPEEFLCLKAIILLNSGAFSFCTGTMEPLHDSTAVQNMLDTITDALIHHISQSGYSAQQQARRQAQLLLLLSHIRHMSNKGMEHLYSMKCKNKVPLYDLLLEMLDAHHLHQPV

来源 Source

来源生物 organism	Melanotaenia fluviatilis
通用名 common_name	Murray River rainbowfish
NCBI Class编号 ncbi_taxonomy_id	120844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	4,4'-PROPANE-2,2-DIYLDIPHENOL
Molecular weight formula_weight	228.3 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

▶

8. Citations (1)

▶

Unit-cell length a length_a	111.569 Å
Unit-cell length b length_b	111.569 Å
Unit-cell length c length_c	99.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	36.520 Å
R factor r_factor	0.1980
R_work r_work	0.1653
R_free r_free	0.1966

fit	/app/data/saxs_computation/n0/9n06/9n06.fit
pddf	/app/data/pr_computation/n0/9n06/9n06.pr.out
profile	/app/data/saxs_computation/n0/9n06/9n06.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Estrogen receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction