SAXSdb — 3vhw

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

Vitamin D3 receptor

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	;methyl (1S,3E)-3-{(2R)-2-[(1R,3aS,4E,7aR)-4-{(2Z)-2-[(3R,4S,5R)-3,5-dihydroxy-4-(3-hydroxypropoxy)-2-methylidenecyclohexylidene]ethylidene}-7a-methyloctahydro-1H-inden-1-yl]propylidene}-1-ethyl-2-oxocyclopentanecarboxylate (non-preferred name) ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VDR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–51； UniProt 118–164 Author chain A； PDBConstruct 52–263； UniProt 216–427

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	3vhw
Deposition date deposition_date	2011-09-08
Structure title title	Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP
Keywords keywords	HORMONE RECEPTOR, TRANSCRIPTION; 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.

3vhw__assembly_1__model_1

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

Download this curve (.dat)

3vhw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vhw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.88 Å
Rg (electron density)	18.66 Å
Total Rg	19.63 Å
Atom count	2063
Residues	254
Excluded volume	37140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vhw__assembly_1__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Vitamin D3 receptor
Molecular weight formula_weight	29805.3 kDa
Mutation mutation	DEL(165-215) mutant
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	2158

GSHMDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS

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	;methyl (1S,3E)-3-{(2R)-2-[(1R,3aS,4E,7aR)-4-{(2Z)-2-[(3R,4S,5R)-3,5-dihydroxy-4-(3-hydroxypropoxy)-2-methylidenecyclohexylidene]ethylidene}-7a-methyloctahydro-1H-inden-1-yl]propylidene}-1-ethyl-2-oxocyclopentanecarboxylate (non-preferred name) ;
Molecular weight formula_weight	570.8 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	95

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3vhwa_
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	3vhwA00
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	44.975 Å
Unit-cell length b length_b	51.470 Å
Unit-cell length c length_c	131.264 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	2.430 Å
Low-resolution limit resolution_low	33.870 Å
R factor r_factor	0.1919
R_work r_work	0.1891
R_free r_free	0.2470

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP

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

Vitamin D3 receptor

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

3vhw__assembly_1__model_1

3vhw__assembly_1__model_1 | I(q)

3vhw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP

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

Vitamin D3 receptor

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

3vhw__assembly_1__model_1

3vhw__assembly_1__model_1 | I(q)

3vhw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)