2HC4

Crystal structure of the LBD of VDR of Danio rerio in complex with calcitriol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 2HC4

Classification: GENE REGULATION

Total Structure Weight: 36253.38

Macromolecule Entities
Molecule Chains Length Organism Details
Vitamin D receptor A 302 Danio rerio Fragment: Ligand binding domain
Gene Name(s): vdra nr1i1a vdr
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SRC-1 from Nuclear receptor coactivator 1 B 15 Homo sapiens EC#: 2.3.1.48 IUBMB
Gene Name(s): NCOA1 Gene View BHLHE74 SRC1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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: 2.2 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.220
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 65.83 α = 90.00
b = 65.83 β = 90.00
c = 264.84 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-15
  • Released Date: 2007-05-01
  • Deposition author(s): Ciesielski, F., Rochel, N., Moras, D.

Revision History

  • Version 1_0: 2007-05-01

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance