1KB4

Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.214

Literature

Macromolecules
Sequence Display for 1KB4

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 37201.40


Macromolecule Entities
Molecule Chains Length Organism Details
Vitamin D3 Receptor A, B 110 Homo sapiens Fragment: DNA-binding Domain (Residues 16-125)
Gene Name(s): VDR Gene View NR1I1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)-3' C 18 synthetic Canonical Direct Repeat with 3 Base Pair Spacer (DR3) Response Element
5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)-3' D 18 synthetic Canonical Direct Repeat with 3 Base Pair Spacer (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: 2.8 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.214
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 61.50 α = 90.00
b = 61.50 β = 90.00
c = 241.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-05
  • Released Date: 2002-05-03
  • Deposition author(s): Shaffer, P.L., Gewirth, D.T.

Revision History

  • Version 1_0: 2002-05-03

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance