4NYA

Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine

Structural Biology Knowledgebase: 4NYA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 4NYA

Classification: RNA

Total Structure Weight: 52777.75

Macromolecule Entities
Molecule Chains Length Organism Details
thiM TPP riboswitch A, B 80 Escherichia coli

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

A, B 5-(azidomethyl)-2-methylpyrimidin-4-amine
C6 H8 N6
HRZOZFYDZBEQQQ-UHFFFAOYSA-N
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)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
A, B NON-POLYMER C10 H16 N5 O14 P3 G
CCC
Query on CCC
A, B RNA LINKING C9 H13 N3 O10 P2 C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.225
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 149.73 α = 90.00
b = 29.89 β = 93.94
c = 95.43 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2013-12-10
  • Released Date: 2014-06-04
  • Deposition author(s): Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Ferre-D'Amare, A.R.

Revision History

No revisions since initial release