3VT3

Crystal structures of rat VDR-LBD with R270L mutation

Structural Biology Knowledgebase: 3VT3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VT3

Classification: HORMONE RECEPTOR

Total Structure Weight: 32692.88

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, R270L
Gene Name(s): Vdr Nr1i1
COACTIVATOR PEPTIDE DRIP C 13 synthetic

Small Molecules
Ligands 3 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.202
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 153.88 α = 90.00
b = 41.63 β = 96.31
c = 41.96 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