3D2G

Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 3D2G

Classification: RNA

Total Structure Weight: 51011.68

Macromolecule Entities
Molecule Chains Length Organism Details
TPP-specific riboswitch A, B 77 Arabidopsis thaliana

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

A, B THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.209
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 76.05 α = 90.00
b = 111.02 β = 90.00
c = 55.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-08
  • Released Date: 2008-07-01
  • Deposition author(s): Thore, S.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4