SAXSdb — 1xap

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

Retinoic acid receptor beta

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 176–421	Fragment：ligand binding domain	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

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 1XAP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HRA THE SOLUTION STRUCTURE OF THE HUMAN RETINOIC ACID RECEPTOR-BETA DNA-BINDING DOMAIN Deposited 1993-07-25	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 75–153（79 aa）	Not recorded	ZN ZINC ION × 2	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
4DM6 Crystal structure of RARb LBD homodimer in complex with TTNPB Deposited 2012-02-07	Different construct Different oligomeric state 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 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 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 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 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 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 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 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 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 22–267； UniProt 176–421

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	1xap
Deposition date deposition_date	2004-08-26
Structure title title	Structure of the ligand binding domain of the Retinoic Acid Receptor beta
Keywords keywords	nuclear receptor, ligand binding domain, retinoic acid receptor beta, TTNPB, 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	18.97 Å
Radius of gyration Rg (electron density) rg_electron	17.69 Å
Forward intensity I(0) i0	11676700.00
Molecular weight molecular_weight	26519.0 kDa
Excluded volume excluded_volume	33716 Å³
Envelope volume envelope_volume	37998 Å³
Hydration-shell volume shell_volume	17982 Å³
Envelope diameter envelope_diameter	61.4 Å
Shell Rg shell_rg	23.83 Å
Envelope Rg envelope_rg	17.95 Å
Shape Rg shape_rg	17.70 Å
Total Rg total_rg	18.61 Å
Total atoms total_atoms	1857
Residues n_residues	232
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	59.7 Å
Rg (real space) rg_real	18.88 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.1680e+07
I(0) uncertainty (real space) i0_real_error	1.4680e+05
Rg (reciprocal space) rg_reciprocal	18.89 Å
I(0) (reciprocal space) i0_reciprocal	11680000.0000
Solution quality estimate total_estimate	0.8188
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.370
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2300000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Retinoic acid receptor beta
Molecular weight formula_weight	30179.0 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	1972

MGSSHHHHHHSSGLVPRGSHMESYEMTAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGHE

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 non-polymer

Description description	4-[(1E)-2-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)PROP-1-ENYL]BENZOIC ACID
Molecular weight formula_weight	348.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1xapa_
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	1xapA00
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	47.276 Å
Unit-cell length b length_b	57.808 Å
Unit-cell length c length_c	90.289 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	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2530

fit	/app/data/saxs_computation/xa/1xap/1xap.fit
pddf	/app/data/pr_computation/xa/1xap/1xap.pr.out
profile	/app/data/saxs_computation/xa/1xap/1xap.dat

Structure of the ligand binding domain of the Retinoic Acid Receptor beta

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

Retinoic acid receptor beta

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