5NEX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 5NEX

Classification: RNA

Total Structure Weight: 6194.54

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 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AG2
Query on AG2

A AGMATINE
(4-AMINOBUTYL)GUANIDINE (Synonym)
C5 H14 N4
QYPPJABKJHAVHS-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: 1.72 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.200
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 55.64 α = 90.00
b = 55.64 β = 90.00
c = 135.93 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-13
  • Released Date: 2017-05-31
  • Deposition author(s): Huang, L., Wang, J., Lilley, D.M.J.

Revision History

  • 2017-07-05
    Type: Database references
  • 2017-08-30
    Type: Author supporting evidence