1YNW

Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding Domains Bound to a DR3 Response Element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 1YNW

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 35710.13


Macromolecule Entities
Molecule Chains Length Organism Details
Vitamin D3 Receptor A 110 Homo sapiens Fragment: DNA-binding Domain (Residues 16-125)
Mutation: P61A, F62A, H75A
Gene Name(s): VDR Gene View NR1I1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Retinoic acid receptor RXR-alpha B 99 Homo sapiens Fragment: DNA-binding Domain (Residues 130-228)
Gene Name(s): RXRA Gene View NR2B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-d(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A)-3' C 18 synthetic DR3 Response Element
5'-d(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A)-3' D 18 synthetic DR3 Response Element

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

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.232
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 123.10 α = 90.00
b = 57.05 β = 110.31
c = 73.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-25
  • Released Date: 2005-02-15
  • Deposition author(s): Shaffer, P.L., Gewirth, D.T.

Revision History

  • Version 1_0: 2005-02-15

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2011-10-26

    Type: Structure summary