3VT8

Crystal structures of rat VDR-LBD with W282R mutation

Structural Biology Knowledgebase: 3VT8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VT8

Classification: HORMONE RECEPTOR

Total Structure Weight: 32597.84

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
COACTIVATOR PEPTIDE DRIP C 13 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YI3
Query on YI3

A (1R,3R,7E,9beta,17beta)-9-butyl-17-[(2R)- 6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra- 5,7-diene-1,3-diol
C30 H52 O3
HGPWGYLACPHOSW-ZOBUFXTASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.189
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 155.07 α = 90.00
b = 42.05 β = 95.62
c = 41.87 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