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9qx6

Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator fragment

Method: X-RAY DIFFRACTION D_max: 56.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qx6
deposition_date	2025-04-15
title	Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator fragment
keywords	RETINOIC ACID RECEPTOR RXR-ALPHA, Nuclear receptor, TRANSCRIPTION; TRANSCRIPTION
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	18.10 Å
rg_electron	17.15 Å
i0	21018000.00
molecular_weight	23689.0 kDa
excluded_volume	23051 Å³
envelope_volume	36155 Å³
shell_volume	17572 Å³
envelope_diameter	56.8 Å
shell_rg	23.39 Å
envelope_rg	17.32 Å
shape_rg	17.14 Å
total_rg	17.89 Å
total_atoms	1796
n_residues	222
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	56.4 Å
rg_real	17.99 Å
rg_real_error	0.28 Å
i0_real	2.1020e+07
i0_real_error	2.3310e+05
rg_reciprocal	18.00 Å
i0_reciprocal	21020000.0000
total_estimate	0.9022
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	22.9 Å
skewness	0.177
kurtosis	-0.453
angular_range	— – 0.4400 Å⁻¹
current_alpha	0.0000
highest_alpha	4844000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Retinoic acid receptor RXR-alpha
formula_weight	26353.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1996

SDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQMT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Nuclear receptor coactivator 2
formula_weight	1276.5 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

HKILHRLLQD

Entity 3 non-polymer

description	(6R,6aR,7S,10R,10aS)-6-(3,5-bis(trifluoromethyl)phenyl)-5,6,6a,7,8,9,10,10a-octahydro-7,10-methanophenanthridine-3-carboxylic acid
formula_weight	455.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	6S,6aS,7R,10S,10aR)-6-(3,5-bis(trifluoromethyl)phenyl)-5,6,6a,7,8,9,10,10a-octahydro-7,10-methanophenanthridine-3-carboxylic acid
formula_weight	455.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	147

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6. Citations (1)

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length_a	64.055 Å
length_b	64.055 Å
length_c	111.626 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	1.460 Å
resolution_low	32.170 Å
r_factor	0.1832
r_work	0.1817
r_free	0.2130

fit	/app/data/saxs_computation/qx/9qx6/9qx6.fit
pddf	/app/data/pr_computation/qx/9qx6/9qx6.pr.out
profile	/app/data/saxs_computation/qx/9qx6/9qx6.dat

Crystal structure of RXR alpha LBD bound to a synthetic agonist FN537 and a coactivator fragment

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)