SAXSdb — 7yxp

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

Ancestral Glucocorticoid Receptor2

unidentified

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 2–248	Not recorded	SHP NR Box 1 Peptide × 1 DEX DEXAMETHASONE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 3.36 Å R-free 0.288

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 7YXP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6W9K Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with Prednisolone and PGC1a coregulator fragment Deposited 2020-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–248（248 aa）	Not recorded	TUA prednisolone × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.2 M ammonium acetate, 3.0 M sodium formate, and 0.1 M HEPES 8.0	Resolution 1.60 Å R-free 0.192
6W9L Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with deacetylated deflazacort and PGC1a coregulator fragment Deposited 2020-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	TUS (4aR,4bS,5S,6aS,6bS,9aR,10aS,10bS)-5-hydroxy-6b-(hydroxyacetyl)-4a,6a,8-trimethyl-4a,4b,5,6,6a,6b,9a,10,10a,10b,11,12-dodecahydro-2H-naphtho[2',1':4,5]indeno[1,2-d][1,3]oxazol-2-one × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.2 M ammonium acetate, 2.5 M sodium formate, and 0.1 M Tris pH 8.5	Resolution 1.45 Å R-free 0.200
6W9M Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with vamorolone and SHP coregulator fragment Deposited 2020-03-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	TUV vamorolone × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289.15 K；25% PEG 300 and 0.1 M Tris pH 8.5	Resolution 1.59 Å R-free 0.220
7YXC Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 PG4 TETRAETHYLENE GLYCOL × 1 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；85 mM sodium cacodylate trihydrate, pH 6.5, 0.17 M sodium acetate trihydrate, 25.5% (w/v) PEG8000, 15% (v/v) glycerol	Resolution 2.25 Å R-free 0.245
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different ligand/ion Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXN Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.46 Å R-free 0.247
7YXN Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.46 Å R-free 0.247
7YXO Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.99 Å R-free 0.280
7YXO Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.99 Å R-free 0.280
7YXO Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.99 Å R-free 0.280
7YXR Crystal structure of mutant AncGR2-LBD (Y545A) bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.50 Å R-free 0.224
7YXR Crystal structure of mutant AncGR2-LBD (Y545A) bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–248（247 aa）	Not recorded	DEX DEXAMETHASONE × 1 FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.50 Å R-free 0.224

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A1X8XLE9_9ZZZZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–248； UniProt 2–248

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	7yxp
Deposition date deposition_date	2022-02-16
Structure title title	Crystal structure of WT AncGR2-LBD WT bound to dexamethasone and SHP coregulator fragment
Keywords keywords	Nuclear Receptor, Transcription Factor, Dexamethasone, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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	19.34 Å
Radius of gyration Rg (electron density) rg_electron	18.06 Å
Forward intensity I(0) i0	14175400.00
Molecular weight molecular_weight	30079.0 kDa
Excluded volume excluded_volume	38405 Å³
Envelope volume envelope_volume	43160 Å³
Hydration-shell volume shell_volume	19631 Å³
Envelope diameter envelope_diameter	63.9 Å
Shell Rg shell_rg	24.86 Å
Envelope Rg envelope_rg	18.44 Å
Shape Rg shape_rg	18.06 Å
Total Rg total_rg	19.07 Å
Total atoms total_atoms	2111
Residues n_residues	254
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	61.5 Å
Rg (real space) rg_real	19.22 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.4180e+07
I(0) uncertainty (real space) i0_real_error	1.8080e+05
Rg (reciprocal space) rg_reciprocal	19.24 Å
I(0) (reciprocal space) i0_reciprocal	14180000.0000
Solution quality estimate total_estimate	0.8142
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4209000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 0.998; 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 (4)

Entity 1 Entity 1 polymer

Description description	Ancestral Glucocorticoid Receptor2
Molecular weight formula_weight	28649.4 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	2111

FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGSVKPLLFHQ

来源 Source

来源生物 organism	unidentified
NCBI Class编号 ncbi_taxonomy_id	32644
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SHP NR Box 1 Peptide
Molecular weight formula_weight	1378.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SRPAILYALLSSS

Entity 3 Entity 3 non-polymer

Description description	DEXAMETHASONE
Molecular weight formula_weight	392.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7yxpA01
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	178.060 Å
Unit-cell length b length_b	178.060 Å
Unit-cell length c length_c	178.060 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	48

Space group space_group	I 41 3 2
Space-group number int_tables_number	214
Crystal system crystal_system	—

Resolution resolution	3.360 Å
Low-resolution limit resolution_low	72.800 Å
R factor r_factor	0.2034
R_work r_work	0.1994
R_free r_free	0.2882

fit	/app/data/saxs_computation/yx/7yxp/7yxp.fit
pddf	/app/data/pr_computation/yx/7yxp/7yxp.pr.out
profile	/app/data/saxs_computation/yx/7yxp/7yxp.dat

Crystal structure of WT AncGR2-LBD WT bound to dexamethasone and SHP coregulator fragment

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

Ancestral Glucocorticoid Receptor2

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 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)