SAXSdb — 7yxo

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

Ancestral Glucocorticoid Receptor2

unidentified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SHP NR Box 1 Peptide × 1 （Q15466） DEXAMETHASONE × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SHP NR Box 1 Peptide × 1 （Q15466） DEXAMETHASONE × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	SHP NR Box 1 Peptide × 1 （Q15466） DEXAMETHASONE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

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 Author chain C； PDBConstruct 2–248； UniProt 2–248 Author chain E； PDBConstruct 2–248； UniProt 2–248

SHP NR Box 1 Peptide

OrganismNot specified

UniProt Q15466

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ancestral Glucocorticoid Receptor2 × 1 （A0A1X8XLE9） DEXAMETHASONE × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ancestral Glucocorticoid Receptor2 × 1 （A0A1X8XLE9） DEXAMETHASONE × 1 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ancestral Glucocorticoid Receptor2 × 1 （A0A1X8XLE9） DEXAMETHASONE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NR0B2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–11； UniProt 17–27 Author chain D； PDBConstruct 1–11； UniProt 17–27 Author chain F； PDBConstruct 1–11； UniProt 17–27

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	7yxo
Deposition date deposition_date	2022-02-16
Structure title title	Crystal structure of WT AncGR2-LBD 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. 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.

7yxo__assembly_1__model_1

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

Download this curve (.dat)

7yxo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7yxo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.19 Å
Rg (electron density)	17.98 Å
Total Rg	19.06 Å
Atom count	2075
Residues	247
Excluded volume	37884 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7yxo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7yxo__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7yxo__assembly_3__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 (6)

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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	6109

FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGSVKPLLFHQ

Source Source

Source organism organism	unidentified
NCBI taxonomy ID ncbi_taxonomy_id	32644
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SHP NR Box 1 Peptide
Molecular weight formula_weight	1204.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

RPAILYALLSS

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	3

Entity 4 Entity 4 non-polymer

Description description	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
Molecular weight formula_weight	614.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7yxoA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	7yxoC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	7yxoE01
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	180.200 Å
Unit-cell length b length_b	180.200 Å
Unit-cell length c length_c	169.180 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 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.990 Å
Low-resolution limit resolution_low	90.100 Å
R factor r_factor	0.2437
R_work r_work	0.2417
R_free r_free	0.2801

Crystal structure of WT AncGR2-LBD 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

SHP NR Box 1 Peptide

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

7yxo__assembly_1__model_1

7yxo__assembly_1__model_1 | I(q)

7yxo__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of WT AncGR2-LBD 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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SHP NR Box 1 Peptide

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

7yxo__assembly_1__model_1

7yxo__assembly_1__model_1 | I(q)

7yxo__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)