3VT6

Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3

Structural Biology Knowledgebase: 3VT6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VT6

Classification: HORMONE RECEPTOR

Total Structure Weight: 32642.91

Macromolecule Entities
Molecule Chains Length Organism Details
Vitamin D3 receptor A 271 Rattus norvegicus Fragment: UNP RESIDUES 116-423
Mutation: ΔS165, ΔY166, ΔS167, ΔP168, ΔR169, ΔP170, ΔT171, ΔL172, ΔS173, ΔF174, ΔS175, ΔG176, ΔN177, ΔS178, ΔS179, ΔS180, ΔS181, ΔS182, ΔS183, ΔD184, ΔL185, ΔY186, ΔT187, ΔT188, ΔS189, ΔL190, ΔD191, ΔM192, ΔM193, ΔE194, ΔP195, ΔS196, ΔG197, ΔF198, ΔS199, ΔN200, ΔL201, ΔD202, ΔL203, ΔN204, ΔG205, ΔE206, ΔD207, ΔS208, ΔD209, ΔD210, ΔP211
Gene Name(s): Vdr Nr1i1
COACTIVATOR PEPTIDE DRIP C 13 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
5YI
Query on 5YI

A (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}- 2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16- triene-1,3-diol
C28 H44 O4 S
PIRFBNFXEQEXIT-XXUXJEHWSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.210
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 153.73 α = 90.00
b = 42.72 β = 95.55
c = 42.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-19
  • Released Date: 2013-05-22
  • Deposition author(s): Nakabayashi, M., Shimizu, M., Ikura, T., Ito, N.

Revision History

  • 2014-02-12
    Type: Citation | Details: Citation update
  • 2013-09-11
    Type: Citation | Details: Citation update