2D5V

Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.245

Literature

Macromolecules
Sequence Display for 2D5V

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 56743.09


Macromolecule Entities
Molecule Chains Length Organism Details
Hepatocyte nuclear factor 6 A, B 164 Rattus norvegicus Fragment: residues 1-156
Gene Name(s): Onecut1 Hnf6 Hnf6a
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' C, E 14 synthetic
5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' D, F 14 synthetic

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

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

D, E ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.245
  • Space Group: P 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 73.02 α = 90.00
b = 38.96 β = 107.63
c = 106.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-07
  • Released Date: 2006-12-05
  • Deposition author(s): Iyaguchi, D., Yao, M., Watanabe, N., Nishihira, J., Tanaka, I.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Non-polymer description, Version format compliance