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9qg3

Human PPAR-gamma ligand binding domain in complex with LW129

Method: X-RAY DIFFRACTION D_max: 85.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qg3
deposition_date	2025-03-13
last_revision	2026-03-25
title	Human PPAR-gamma ligand binding domain in complex with LW129
keywords	;PPAR, PPAR gamma, PPARg, peroxisome proliferator-activated receptor gamma, nuclear receptor, transcription factor, partial agonist, agonist, 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	25.79 Å
rg_electron	25.01 Å
i0	100743000.00
molecular_weight	53797.0 kDa
excluded_volume	52612 Å³
envelope_volume	88230 Å³
shell_volume	29293 Å³
envelope_diameter	89.2 Å
shell_rg	32.15 Å
envelope_rg	25.08 Å
shape_rg	24.96 Å
total_rg	25.69 Å
total_atoms	4076
n_residues	521
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	85.7 Å
rg_real	25.73 Å
rg_real_error	0.67 Å
i0_real	1.0070e+08
i0_real_error	1.5270e+06
rg_reciprocal	25.75 Å
i0_reciprocal	100700000.0000
total_estimate	0.8883
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.4 Å
skewness	0.279
kurtosis	-0.377
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	19820000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Peroxisome proliferator-activated receptor gamma
formula_weight	31410.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	4104

GSHMESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	4-[5-chloranyl-1-[2-chloranyl-6-(trifluoromethyl)phenyl]carbonyl-indazol-3-yl]-2-fluoranyl-3-phenylmethoxy-benzoic acid
formula_weight	603.3 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	28

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6. Citations (1)

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length_a	92.778 Å
length_b	60.953 Å
length_c	118.394 Å
angle_alpha	90.00 °
angle_beta	101.92 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.300 Å
resolution_low	27.550 Å
r_factor	0.2147
r_work	0.2125
r_free	0.2549

fit	/app/data/saxs_computation/qg/9qg3/9qg3.fit
pddf	/app/data/pr_computation/qg/9qg3/9qg3.pr.out
profile	/app/data/saxs_computation/qg/9qg3/9qg3.dat

Human PPAR-gamma ligand binding domain in complex with LW129

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