8pwd

Crystal structure of VDR in complex Des-C-Ring and Aromatic-D-Ring analog 3c

Method: X-RAY DIFFRACTION Dmax: 62.3 Å Quality: GOOD

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

Vitamin D3 receptor A

Danio rerio

UniProt Q9PTN2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 156–453 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) FT9 (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)hept-3-ynyl]phenyl]pent-2-enylidene]cyclohexane-1,3-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;NH4SO4 1.5M, BisTris 0.1M pH 7 Resolution 2.80 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

74 other PDB entries and 74 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VDRA_DANRE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–302; UniProt 156–453

Nuclear receptor coactivator 2

OrganismNot specified

UniProt Q15596

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 686–698 Not recorded Vitamin D3 receptor A × 2 (Q9PTN2) FT9 (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)hept-3-ynyl]phenyl]pent-2-enylidene]cyclohexane-1,3-diol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;NH4SO4 1.5M, BisTris 0.1M pH 7 Resolution 2.80 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

283 other PDB entries and 334 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCOA2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–13; UniProt 686–698

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8pwd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8pwd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8pwd
Deposition date deposition_date2023-07-20
Structure title titleCrystal structure of VDR in complex Des-C-Ring and Aromatic-D-Ring analog 3c
Keywords keywordsnuclear receptor, VDR, agonist, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.38
Radius of gyration Rg (electron density) rg_electron18.07
Forward intensity I(0) i014074400.00
Molecular weight molecular_weight28756.0 kDa
Excluded volume excluded_volume36311 ų
Envelope volume envelope_volume41993 ų
Hydration-shell volume shell_volume19271 ų
Envelope diameter envelope_diameter63.8
Shell Rg shell_rg24.47
Envelope Rg envelope_rg18.29
Shape Rg shape_rg18.04
Total Rg total_rg19.14
Total atoms total_atoms2019
Residues n_residues246
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.3
Rg (real space) rg_real19.26
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real1.4070e+07
I(0) uncertainty (real space) i0_real_error1.7540e+05
Rg (reciprocal space) rg_reciprocal19.28
I(0) (reciprocal space) i0_reciprocal14070000.0000
Solution quality estimate total_estimate0.8037
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.6
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.331
Angular range angular_range— – 0.4100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3135000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.816; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)