SAXSdb — 9m1d

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

Vitamin D3 receptor

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Mediator of RNA polymerase II transcription subunit 1 × 1 （Q15648） (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-methyl-propyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VDR_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–271； UniProt 116–423

Mediator of RNA polymerase II transcription subunit 1

OrganismNot specified

UniProt Q15648

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Vitamin D3 receptor × 1 （P13053） (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-methyl-propyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MED1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–13； UniProt 640–652

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	9m1d
Deposition date deposition_date	2025-02-25
Structure title title	Vitamin D receptor complex with a methyldiphenylpropylsilane derivative
Keywords keywords	Vitamin D 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.

9m1d__assembly_1__model_1

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

Download this curve (.dat)

9m1d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9m1d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.27 Å
Rg (electron density)	18.06 Å
Total Rg	19.15 Å
Atom count	2051
Residues	251
Excluded volume	36735 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9m1d__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Vitamin D3 receptor
Molecular weight formula_weight	30595.0 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	2452

GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGSVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Mediator of RNA polymerase II transcription subunit 1
Molecular weight formula_weight	1570.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KNHPMLMNLLKDN

Entity 3 Entity 3 non-polymer

Description description	(4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-methyl-propyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid
Molecular weight formula_weight	516.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	217

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Unit-cell length a length_a	154.850 Å
Unit-cell length b length_b	42.210 Å
Unit-cell length c length_c	42.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.440 Å
Low-resolution limit resolution_low	38.580 Å
R factor r_factor	0.1799
R_work r_work	0.1786
R_free r_free	0.2104

Vitamin D receptor complex with a methyldiphenylpropylsilane derivative

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

Mediator of RNA polymerase II transcription subunit 1

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

9m1d__assembly_1__model_1

9m1d__assembly_1__model_1 | I(q)

9m1d__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 (4)

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 water

7. Citations (1)

Vitamin D receptor complex with a methyldiphenylpropylsilane derivative

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

Mediator of RNA polymerase II transcription subunit 1

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

9m1d__assembly_1__model_1

9m1d__assembly_1__model_1 | I(q)

9m1d__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 (4)

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 water

7. Citations (1)