3K0J

Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 3K0J

Classification: RNA / RNA BINDING PROTEIN

Total Structure Weight: 101404.16


Macromolecule Entities
Molecule Chains Length Organism Details
U1 small nuclear ribonucleoprotein A A, B, C, D 96 Homo sapiens Fragment: UNP residues 2-97, RRM 1 domain
Mutation: Y231H, Q236R
Gene Name(s): SNRPA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (87-MER) E, F 87 synthetic

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

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

E, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TPP N/A in BindingDB
N/A in BindingMoad
Kd: 8.65 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.197
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 52.25 α = 90.00
b = 71.60 β = 94.62
c = 128.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-24
  • Released Date: 2009-12-22
  • Deposition author(s): Kulshina, N., Edwards, T.E., Ferre-D'Amare, A.R.

Revision History

  • 2011-07-13
    Type: Version format compliance