1DB1

CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D

Structural Biology Knowledgebase: 1DB1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1DB1

Classification: GENE REGULATION

Total Structure Weight: 29808.70

Macromolecule Entities
Molecule Chains Length Organism Details
VITAMIN D NUCLEAR RECEPTOR A 259 Homo sapiens Fragment: LIGAND BINDING DOMAIN
Gene Name(s): VDR Gene View NR1I1

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VDX N/A in BindingDB
Kd: 0.55 nM  BindingMOAD
Kd: 0.55 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.191
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.19 α = 90.00
b = 52.44 β = 90.00
c = 133.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-02
  • Released Date: 2000-01-31
  • Deposition author(s): Rochel, N., Wurtz, J.M., Mitschler, A., Klaholz, B., Moras, D.

Revision History

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