3VT9

Crystal structures of rat VDR-LBD with W282R mutation

Structural Biology Knowledgebase: 3VT9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 3VT9

Classification: HORMONE RECEPTOR

Total Structure Weight: 32623.87

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, W282R
Gene Name(s): Vdr Nr1i1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
COACTIVATOR PEPTIDE DRIP C 13 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YI4
Query on YI4

A (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)- 17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9- (prop-2-en-1-yl)-9,10-secoestra-5,7-diene- 1,3-diol
C31 H50 O4
VQPYCEUJPLIUFQ-ZVOFGSMJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.198
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 154.71 α = 90.00
b = 42.05 β = 95.63
c = 41.97 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