2GDI

Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate

  • Classification: RNA
  • Deposited: 2006-03-16 Released: 2006-07-04
  • Deposition author(s): Serganov, A.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 2GDI

Classification: RNA

Total Structure Weight: 53244.23

Macromolecule Entities
Molecule Chains Length Organism Details
TPP riboswitch X, Y 80 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TPP
Query on TPP

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

X POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

X, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

X SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
X, Y NON-POLYMER C10 H16 N5 O14 P3 G
CCC
Query on CCC
X, Y RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.208
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 148.82 α = 90.00
b = 29.56 β = 94.55
c = 95.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-16
  • Released Date: 2006-07-04
  • Deposition author(s): Serganov, A.

Revision History

  • Version 1_0: 2006-07-04

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance