5GT4

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol

Takimoto-Kamimura, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
255Homo sapiensMutation(s): 0 
Gene Names: VDRNR1I1
Find proteins for P11473 (Homo sapiens)
Go to UniProtKB:  P11473
NIH Common Fund Data Resources
PHAROS  P11473
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2KB
Query on 2KB

Download CCD File 
A
4-{[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}butanenitrile
C31 H49 N O4
KQWXEWOYVIUCOD-IBOBMRDDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.663α = 90
b = 51.842β = 90
c = 131.475γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-08-18 
  • Released Date: 2016-11-09 
  • Deposition Author(s): Takimoto-Kamimura, M.
  • This entry supersedes: 4PA2

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations