SAXSdb — 1hra

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

RETINOIC ACID RECEPTOR

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 75–153	Not recorded	ZN ZINC ION × 2	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1HRA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XAP Structure of the ligand binding domain of the Retinoic Acid Receptor beta Deposited 2004-08-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 176–421（246 aa） Fragment：ligand binding domain	Not recorded	TTB 4-[(1E)-2-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PROP-1-ENYL]BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；PEG 8000, potassium chloride, magnesium chloride, MES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.10 Å R-free 0.253
4DM6 Crystal structure of RARb LBD homodimer in complex with TTNPB Deposited 2012-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 176–421（246 aa） Fragment：unp residues 176-421	Not recorded	TTB 4-[(1E)-2-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PROP-1-ENYL]BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；5% polyethylene glycol 8000, 0.2 M KCl, 0.01 M MgCl2 and 0.05 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 5.6	Resolution 1.90 Å R-free 0.239
4DM6 Crystal structure of RARb LBD homodimer in complex with TTNPB Deposited 2012-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 176–421（246 aa） Fragment：unp residues 176-421	Not recorded	TTB 4-[(1E)-2-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PROP-1-ENYL]BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；5% polyethylene glycol 8000, 0.2 M KCl, 0.01 M MgCl2 and 0.05 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 5.6	Resolution 1.90 Å R-free 0.239
4DM8 Crystal structure of RARb LBD in complex with 9cis retinoic acid Deposited 2012-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 176–421（246 aa） Fragment：unp residues 176-421	Not recorded	REA RETINOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；5% polyethylene glycol 8000, 0.2 M KCl, 0.01 M MgCl2 and 0.05 M MES pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.277
4DM8 Crystal structure of RARb LBD in complex with 9cis retinoic acid Deposited 2012-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 176–421（246 aa） Fragment：unp residues 176-421	Not recorded	REA RETINOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；5% polyethylene glycol 8000, 0.2 M KCl, 0.01 M MgCl2 and 0.05 M MES pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.277
4JYG Crystal structure of RARbeta LBD in complex with agonist BMS411 [4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid] Deposited 2013-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 176–421（246 aa） Fragment：Ligand binding domain, UNP residues 176-421 Chain B 176–421（246 aa） Fragment：Ligand binding domain, UNP residues 176-421	Not recorded	1NY 4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid × 2 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；291 K；200 mM Tri Sodium Citrate pH 5.5, 25 % PEG 4000, VAPOR DIFFUSION, temperature 291K	Resolution 2.35 Å R-free 0.257
4JYH Crystal structure of RARbeta LBD in complex with selective agonist BMS948 [4-{[(8-phenylnaphthalen-2-yl)carbonyl]amino}benzoic acid] Deposited 2013-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 176–421（246 aa） Fragment：Ligand binding domain, UNP residues 176-421 Chain B 176–421（246 aa） Fragment：Ligand binding domain, UNP residues 176-421	Not recorded	JYH 4-{[(8-phenylnaphthalen-2-yl)carbonyl]amino}benzoic acid × 2 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；291 K；200 mM Tri Sodium Citrate pH 5.5, 25% PEG 4000, VAPOR DIFFUSION, temperature 291K	Resolution 2.60 Å R-free 0.267
4JYI Crystal structure of RARbeta LBD in complex with selective partial agonist BMS641 [3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid] Deposited 2013-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 176–421（246 aa） Fragment：Ligand binding domain, UNP residues 176-421 Chain B 176–421（246 aa） Fragment：Ligand binding domain, UNP residues 176-421	Not recorded	JYI 3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid × 2 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；291 K；200 mM Tri Sodium Citrate pH 5.5, 25% PEG 4000, VAPOR DIFFUSION, temperature 291K	Resolution 1.90 Å R-free 0.227
5UAN Crystal structure of multi-domain RAR-beta-RXR-alpha heterodimer on DNA Deposited 2016-12-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 80–455（376 aa） Fragment：UNP residues 98-462	Not recorded	ZN ZINC ION × 4 9CR (9cis)-retinoic acid × 1 REA RETINOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；MES, PEG300	Resolution 3.51 Å R-free 0.270
6SSQ Crystal structure of RARbeta LBD in complex with LG 100754 Deposited 2019-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 176–421（246 aa） Chain B 176–421（246 aa）	Not recorded	754 (2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5,6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid × 2 FLC CITRATE ANION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；200 mM Tri Sodium Citrate pH 5.5, 25 % PEG 4000	Resolution 2.30 Å R-free 0.208

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RARB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–80； UniProt 75–153

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	1hra
Deposition date deposition_date	1993-07-25
Structure title title	THE SOLUTION STRUCTURE OF THE HUMAN RETINOIC ACID RECEPTOR-BETA DNA-BINDING DOMAIN
Keywords keywords	DNA-BINDING RECEPTOR; DNA-BINDING RECEPTOR
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	11.75 Å
Radius of gyration Rg (electron density) rg_electron	11.91 Å
Forward intensity I(0) i0	344638000.00
Molecular weight molecular_weight	143370.0 kDa
Excluded volume excluded_volume	174060 Å³
Envelope volume envelope_volume	17613 Å³
Hydration-shell volume shell_volume	11275 Å³
Envelope diameter envelope_diameter	45.8 Å
Shell Rg shell_rg	19.07 Å
Envelope Rg envelope_rg	13.68 Å
Shape Rg shape_rg	11.95 Å
Total Rg total_rg	11.94 Å
Total atoms total_atoms	9810
Residues n_residues	1200
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	41.0 Å
Rg (real space) rg_real	11.69 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	3.4460e+08
I(0) uncertainty (real space) i0_real_error	3.7320e+06
Rg (reciprocal space) rg_reciprocal	11.69 Å
I(0) (reciprocal space) i0_reciprocal	344600000.0000
Solution quality estimate total_estimate	0.8738
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.5 Å
Skewness Skewness skewness	0.157
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	117300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1hraa_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

CATH v4.4 (1 domains)

Domain ID domain_id	1hraA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

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8. Citations (3)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	RETINOIC ACID RECEPTOR
Molecular weight formula_weight	9434.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9810

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

THE SOLUTION STRUCTURE OF THE HUMAN RETINOIC ACID RECEPTOR-BETA DNA-BINDING DOMAIN

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

RETINOIC ACID RECEPTOR

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

fit	/app/data/saxs_computation/hr/1hra/1hra.fit
pddf	/app/data/pr_computation/hr/1hra/1hra.pr.out
profile	/app/data/saxs_computation/hr/1hra/1hra.dat