5GT4 | pdb_00005gt4

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

• PDB DOI: https://doi.org/10.2210/pdb5GT4/pdb
• Entry: 5GT4 supersedes: 4PA2

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


• Deposited: 2016-08-18 Released: 2016-11-09 
• Deposition Author(s): Takimoto-Kamimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.45 kDa 
• Atom Count: 2,171 
• Modeled Residue Count: 255 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	255	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
2KB	B [auth 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.663	α = 90
b = 51.842	β = 90
c = 131.475	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description