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9v8h

PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone

Method: X-RAY DIFFRACTION D_max: 62.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v8h
deposition_date	2025-05-29
title	PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone
keywords	Nuclear receptor, de novo peptide, 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	19.89 Å
rg_electron	18.62 Å
i0	14750800.00
molecular_weight	30684.0 kDa
excluded_volume	39280 Å³
envelope_volume	44500 Å³
shell_volume	19884 Å³
envelope_diameter	64.4 Å
shell_rg	25.05 Å
envelope_rg	18.86 Å
shape_rg	18.59 Å
total_rg	19.73 Å
total_atoms	2158
n_residues	262
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	62.9 Å
rg_real	19.78 Å
rg_real_error	0.32 Å
i0_real	1.4750e+07
i0_real_error	1.8390e+05
rg_reciprocal	19.79 Å
i0_reciprocal	14750000.0000
total_estimate	0.8958
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.8 Å
skewness	0.212
kurtosis	-0.371
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	3697000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.979

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Peroxisome proliferator-activated receptor gamma
formula_weight	31449.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2434

QLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	PG08-NL
formula_weight	2133.6 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

YKTANSVXVRHXLLTAILXX

Entity 3 non-polymer

description	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
formula_weight	357.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	243

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6. Citations (1)

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length_a	43.690 Å
length_b	53.470 Å
length_c	66.830 Å
angle_alpha	90.00 °
angle_beta	106.50 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.390 Å
resolution_low	32.060 Å
r_factor	0.1638
r_work	0.1629
r_free	0.1900

fit	/app/data/saxs_computation/v8/9v8h/9v8h.fit
pddf	/app/data/pr_computation/v8/9v8h/9v8h.pr.out
profile	/app/data/saxs_computation/v8/9v8h/9v8h.dat

PPARgamma ligand-binding domain in complex with PG08-NL and rosiglitazone

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)