5NEF

The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with guanidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 5NEF

Classification: RNA

Total Structure Weight: 6173.51

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3') A 18 Gloeobacter violaceus

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAI
Query on GAI

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

A 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 RNA LINKING C9 H13 Br N3 O8 P C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.203
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 55.70 α = 90.00
b = 55.70 β = 90.00
c = 132.56 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-10
  • Released Date: 2017-06-07
  • Deposition author(s): Huang, L., Wang, J., Lilley, D.M.J.

Revision History

No revisions since initial release