SAXSdb — 2hfp

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 234–505	Fragment：Ligand Binding Domain (residues 234-505)	SRC Peptide Fragment × 1 （Q2T9G5） NSI 3-(4-METHOXYPHENYL)-N-(PHENYLSULFONYL)-1-[3-(TRIFLUOROMETHYL)BENZYL]-1H-INDOLE-2-CARBOXAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：298 K；Two microliters of protein solution (10 mg/mL, 1 peptide fragment) was added to two microliters of well (2% Peg400, 1.6 Molar ammonium sulfate, 100 mM Mes 6.5) and hung over 1000 microliters well in a 2 + 2 hanging drop crystallization setup , temperature 298.0K	Resolution 2.00 Å R-free 0.285

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 2HFP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2G0H Structure-based drug design of a novel family of PPAR partial agonists: virtual screening, x-ray crystallography and in vitro/in vivo biological activities Deposited 2006-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 235–505（271 aa） Fragment：Ligand binding domain(residues 207-477) Chain B 235–505（271 aa） Fragment：Ligand binding domain(residues 207-477)	Not recorded	SP3 N-[1-(4-FLUOROPHENYL)-3-(2-THIENYL)-1H-PYRAZOL-5-YL]-3,5-BIS(TRIFLUOROMETHYL)BENZENESULFONAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；20% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.293

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPARG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–282； UniProt 234–505

SRC Peptide Fragment

OrganismNot specified

UniProt Q2T9G5

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 680–700	Not recorded	Peroxisome proliferator-activated receptor gamma × 1 （Q86U60） NSI 3-(4-METHOXYPHENYL)-N-(PHENYLSULFONYL)-1-[3-(TRIFLUOROMETHYL)BENZYL]-1H-INDOLE-2-CARBOXAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：298 K；Two microliters of protein solution (10 mg/mL, 1 peptide fragment) was added to two microliters of well (2% Peg400, 1.6 Molar ammonium sulfate, 100 mM Mes 6.5) and hung over 1000 microliters well in a 2 + 2 hanging drop crystallization setup , temperature 298.0K	Resolution 2.00 Å R-free 0.285

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 2HFP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NPA the crystal structure of the human PPARaplpha ligand binding domain in complex with a a-hydroxyimino phenylpropanoic acid Deposited 2006-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 683–697（15 aa）	Not recorded	MMB (2R,3E)-2-{4-[(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)METHOXY]BENZYL}-3-(PROPOXYIMINO)BUTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；6% PEG 10K. 0.1M Hepes, 6% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.260
2NPA the crystal structure of the human PPARaplpha ligand binding domain in complex with a a-hydroxyimino phenylpropanoic acid Deposited 2006-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 683–697（15 aa）	Not recorded	MMB (2R,3E)-2-{4-[(5-METHYL-2-PHENYL-1,3-OXAZOL-4-YL)METHOXY]BENZYL}-3-(PROPOXYIMINO)BUTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；6% PEG 10K. 0.1M Hepes, 6% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.30 Å R-free 0.260

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q2T9G5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–21； UniProt 680–700

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	2hfp
Deposition date deposition_date	2006-06-25
Structure title title	Crystal Structure of PPAR Gamma with N-sulfonyl-2-indole carboxamide ligands
Keywords keywords	PPAR PPARGamma LBD, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.39 Å
Radius of gyration Rg (electron density) rg_electron	19.09 Å
Forward intensity I(0) i0	18438000.00
Molecular weight molecular_weight	34183.0 kDa
Excluded volume excluded_volume	43532 Å³
Envelope volume envelope_volume	49579 Å³
Hydration-shell volume shell_volume	21342 Å³
Envelope diameter envelope_diameter	64.1 Å
Shell Rg shell_rg	25.77 Å
Envelope Rg envelope_rg	19.32 Å
Shape Rg shape_rg	19.06 Å
Total Rg total_rg	20.18 Å
Total atoms total_atoms	2406
Residues n_residues	289
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

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

Maximum dimension Dmax dmax	63.2 Å
Rg (real space) rg_real	20.27 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	1.8440e+07
I(0) uncertainty (real space) i0_real_error	2.3420e+05
Rg (reciprocal space) rg_reciprocal	20.30 Å
I(0) (reciprocal space) i0_reciprocal	18440000.0000
Solution quality estimate total_estimate	0.9005
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.167
Kurtosis Kurtosis kurtosis	-0.437
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4429000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Peroxisome proliferator-activated receptor gamma
Molecular weight formula_weight	32467.6 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	2528

MSYYHHHHHHPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	SRC Peptide Fragment
Molecular weight formula_weight	2431.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

HSSLTERHKILHRLLQEGSPS

Entity 3 Entity 3 non-polymer

Description description	3-(4-METHOXYPHENYL)-N-(PHENYLSULFONYL)-1-[3-(TRIFLUOROMETHYL)BENZYL]-1H-INDOLE-2-CARBOXAMIDE
Molecular weight formula_weight	564.6 kDa
Source method src_method	syn
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	122

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2hfpa_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (1 domains)

Domain ID domain_id	2hfpA00
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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8. Citations (1)

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Unit-cell length a length_a	46.487 Å
Unit-cell length b length_b	77.178 Å
Unit-cell length c length_c	82.075 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	39.800 Å
R factor r_factor	0.2090
R_work r_work	0.2050
R_free r_free	0.2850

fit	/app/data/saxs_computation/hf/2hfp/2hfp.fit
pddf	/app/data/pr_computation/hf/2hfp/2hfp.pr.out
profile	/app/data/saxs_computation/hf/2hfp/2hfp.dat

Crystal Structure of PPAR Gamma with N-sulfonyl-2-indole carboxamide ligands

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

SRC Peptide Fragment

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)