4NYD

Crystal structure of the E. coli thiM riboswitch in complex with hypoxanthine

Structural Biology Knowledgebase: 4NYD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 4NYD

Classification: RNA

Total Structure Weight: 27362.77

Macromolecule Entities
Molecule Chains Length Organism Details
thiM TPP riboswitch A 83 Escherichia coli

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

A HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
A23
Query on A23
A RNA LINKING C10 H13 N5 O9 P2 A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.200
  • Space Group: P 32 1 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.44 α = 90.00
b = 65.44 β = 90.00
c = 101.11 γ = 120.00

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