5NDH

The structure of the G. violaceus guanidine II riboswitch P2 stem-loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 5NDH

Classification: RNA

Total Structure Weight: 21524.92

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3') A, B, C, D 16 Gloeobacter violaceus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

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

A, B, C, D GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-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)
NA
Query on NA

A, B, C 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: 1.81 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.207
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 48.73 α = 90.00
b = 57.83 β = 90.00
c = 100.86 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

  • Version 1_0: 2017-05-31

    Type: Initial release

  • Version 1_1: 2017-07-05

    Type: Database references

  • Version 1_2: 2017-08-30

    Type: Author supporting evidence