3VT7

Crystal structures of rat VDR-LBD with W282R mutation

Structural Biology Knowledgebase: 3VT7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 3VT7

Classification: HORMONE RECEPTOR

Total Structure Weight: 32553.78

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
VDX
Query on VDX

A 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A- METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}- 4-METHYLENE-CYCLOHEXANE-1,3-DIOL
1,25 DIHYDROXY VITAMIN D3 (Synonym)
C27 H44 O3
GMRQFYUYWCNGIN-NKMMMXOESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.185
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 155.14 α = 90.00
b = 42.28 β = 95.53
c = 41.85 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