SAXSdb — 6ad9

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

Peroxisome proliferator-activated receptor gamma

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha × 1 （Q9UBK2） 3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl)methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPARG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–287； UniProt 223–505

12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha

OrganismNot specified

UniProt Q9UBK2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peroxisome proliferator-activated receptor gamma × 1 （P37231） 3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl)methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRGC1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 141–152

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ad9
Deposition date deposition_date	2018-07-31
Structure title title	Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9
Keywords keywords	PPARgamma Ligand Binding Domain Agonist, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6ad9__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6ad9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ad9__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.91 Å
Rg (electron density)	18.66 Å
Total Rg	19.76 Å
Atom count	2152
Residues	265
Excluded volume	39187 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ad9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Peroxisome proliferator-activated receptor gamma
Molecular weight formula_weight	32693.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2339

GSHMAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Molecular weight formula_weight	1265.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PSLLKKLLLAPA

Entity 3 Entity 3 non-polymer

Description description	3-[(1E)-1-{8-[(4-methyl-2-propyl-1H-benzimidazol-1-yl)methyl]dibenzo[b,e]oxepin-11(6H)-ylidene}ethyl]-1,2,4-oxadiazol-5(4H)-one
Molecular weight formula_weight	492.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6ad9A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

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Unit-cell length a length_a	43.730 Å
Unit-cell length b length_b	54.338 Å
Unit-cell length c length_c	66.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1874
R_work r_work	0.1845
R_free r_free	0.2399

Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9

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

Peroxisome proliferator-activated receptor gamma

State in the Current Structure

Other States of the Same Protein in the Database

12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ad9__assembly_1__model_1

6ad9__assembly_1__model_1 | I(q)

6ad9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-9

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

Peroxisome proliferator-activated receptor gamma

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

12-mer peptide from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ad9__assembly_1__model_1

6ad9__assembly_1__model_1 | I(q)

6ad9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)