5XUQ | pdb_00005xuq

Crystal structure of VDR-LBD complexed with an antagonist, 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin D3

• PDB DOI: https://doi.org/10.2210/pdb5XUQ/pdb

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


• Deposited: 2017-06-24 Released: 2018-06-27 
• Deposition Author(s): Kato, A., Itoh, T., Yamamoto, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.196 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Discovery of Potent Vitamin D Receptor Antagonist

Kato, A., Tabei, M., Itoh, T., Yamamoto, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.67 kDa 
• Atom Count: 1,959 
• Modeled Residue Count: 241 
• Deposited Residue Count: 284 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	271	Rattus norvegicus	Mutation(s): 0  Gene Names: Vdr, Nr1i1
UniProt
Find proteins for P13053 (Rattus norvegicus) Explore P13053  Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 1	B [auth C]	13	Homo sapiens	Mutation(s): 0  Gene Names:  MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648  Go to UniProtKB:  Q15648
PHAROS:  Q15648 GTEx:  ENSG00000125686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8FF	C [auth A]	(4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(1~{H}-pyrrol-2-yl)octan-1-one C33 H49 N O3 LSFVNCITLLLHBJ-LTRSXRPOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.196 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.8	α = 90
b = 41.49	β = 96.97
c = 42.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Kato, A., Itoh, T., Yamamoto, K.

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Refinement description