5NDI

The structure of the E.coli guanidine II riboswitch P1 stem-loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 5NDI

Classification: RNA

Total Structure Weight: 26202.37

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*(CBV)P*AP*AP*A)-3') A, B, C, D 20 Escherichia coli

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

A, B, C, D GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CBV
Query on CBV
A, B, C, D RNA LINKING C9 H13 Br N3 O8 P C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.188
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 47.48 α = 90.00
b = 48.19 β = 90.00
c = 153.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-08
  • Released Date: 2017-05-31
  • Deposition author(s): Huang, L., Wang, J., Lilley, D.M.J.

Revision History

No revisions since initial release