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

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)

Starting Model: experimental
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Literature

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

Kakuda, S.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11473
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SV0 (Subject of Investigation/LOI) Query on SV0 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.