SAXSdb — 5y41

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

Nuclear receptor subfamily 4 group A member 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid × 1 TRIETHYLENE GLYCOL × 1 DI(HYDROXYETHYL)ETHER × 1 CHLORIDE ION × 1 MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	(13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid × 2 TRIETHYLENE GLYCOL × 1 DI(HYDROXYETHYL)ETHER × 1 CHLORIDE ION × 2 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NR4A2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 328–598 Author chain B； PDBConstruct 1–271； UniProt 328–598

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	5y41
Deposition date deposition_date	2017-07-31
Structure title title	Crystal Structure of LIGAND-BOUND NURR1-LBD
Keywords keywords	Nurr1, LBD, Prostaglandin, TRANSCRIPTION, MICHAEL ADDITION; TRANSCRIPTION
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.

5y41__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5y41__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5y41__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.24 Å
Rg (electron density)	24.44 Å
Total Rg	25.25 Å
Atom count	3764
Residues	464
Excluded volume	67905 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5y41__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5y41__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5y41__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 (7)

Entity 1 Entity 1 polymer

Description description	Nuclear receptor subfamily 4 group A member 2
Molecular weight formula_weight	30576.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4082

MVKEVVRTDSLKGRRGRLPSKPKSPQEPSPPSPPVSLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVTERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFLDTLPF

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(13E,15S)-15-hydroxy-9-oxoprosta-10,13-dien-1-oic acid
Molecular weight formula_weight	336.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5y41a_
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

Domain ID domain_id	d5y41b_
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 (2 domains)

Domain ID domain_id	5y41A00
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	5y41B00
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	88.520 Å
Unit-cell length b length_b	131.460 Å
Unit-cell length c length_c	47.130 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2072
R_work r_work	0.2057
R_free r_free	0.2529

Crystal Structure of LIGAND-BOUND NURR1-LBD

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

Nuclear receptor subfamily 4 group A member 2

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

5y41__assembly_3__model_1

5y41__assembly_3__model_1 | I(q)

5y41__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of LIGAND-BOUND NURR1-LBD

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

Nuclear receptor subfamily 4 group A member 2

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

5y41__assembly_3__model_1

5y41__assembly_3__model_1 | I(q)

5y41__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)