2HBH

Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide

Structural Biology Knowledgebase: 2HBH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2HBH

Classification: GENE REGULATION

Total Structure Weight: 36231.54

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
XE4
Query on XE4

A 1,3-CYCLOHEXANEDIOL, 4-METHYLENE-5-[(2E)- [(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL- 1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]- , (1R,3S,5Z)
23-DIYNE, (Synonym)
C26 H34 O3
CEEUUHVULXTFGS-BQXVGYHGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.203
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.68 α = 90.00
b = 65.68 β = 90.00
c = 265.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-14
  • Released Date: 2007-05-01
  • Deposition author(s): Rochel, N., Hourai, S., Moras, D.

Revision History

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