8IQT | pdb_00008iqt

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3

• PDB DOI: https://doi.org/10.2210/pdb8IQT/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-17 Released: 2024-03-27 
• Deposition Author(s): Kakuda, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3

Kakuda, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.82 kDa 
• Atom Count: 2,160 
• Modeled Residue Count: 254 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	306	Homo sapiens	Mutation(s): 0  Gene Names: VDR, NR1I1
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473  Go to UniProtKB:  P11473
PHAROS:  P11473 GTEx:  ENSG00000111424

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SV0 (Subject of Investigation/LOI)	B [auth A]	(1~{S},3~{Z})-3-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},4~{R})-4-fluoranyl-6-methyl-6-oxidanyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol C27 H43 F O2 GFRHQHOVEZIWBD-VCAQAZSGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.723	α = 90
b = 51.363	β = 90
c = 132.102	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Kakuda, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release