2HCD

Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide

Structural Biology Knowledgebase: 2HCD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2HCD

Classification: GENE REGULATION

Total Structure Weight: 36339.78

Macromolecule Entities
Molecule Chains Length Organism Details
Vitamin D receptor A 302 Danio rerio Fragment: Ligand binding domain
Gene Name(s): vdra nr1i1a vdr
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

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

A 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE- 1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)- , (1A,3B,5Z,7E)
GEMINI (Synonym)
C32 H54 O4
WTQXZYVWLNPNEX-LKUPKUSPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.204
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.86 α = 90.00
b = 65.86 β = 90.00
c = 265.02 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-16
  • Released Date: 2007-05-01
  • Deposition author(s): Ciesielski, F., Rochel, N., Moras, D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4