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5v39

Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vitamin D3 receptor

Homo sapiens

UniProt P11473

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 5-(3-{4-[(2S)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-3-methyl-N-(1H-tetrazol-5-yl)thiophene-2-carboxamide × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1db1 1ie8 1ie9 1s0z 1s19 1txi 2ham 2har 2has 2hb7 2hb8 3a2i

48 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1kb2 1kb4 1kb6 1ynw

4 assemblies

View Construct and Data Evidence
UniProt name VDR_HUMAN
Isoform P11473-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–256； UniProt 169–475

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_id5v39
Deposition date deposition_date2017-03-06
Structure title titleCrystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM
Keywords keywordsVDR, LBD, VDRM, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-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.

5v39__assembly_1__model_1

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

Download this curve (.dat)

5v39__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5v39__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）19.61 Å
Rg (electron density)18.45 Å
Total Rg19.44 Å
Atom count2025
Residues251
Excluded volume36383 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5v39__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)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5v39a_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (1 domains)

Domain ID domain_id5v39A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
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7. Citations (1)