5U3G

Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 5U3G

Classification: RNA

Total Structure Weight: 28595.11

Macromolecule Entities
Molecule Chains Length Organism Details
ykkC riboswitch B 85 Dickeya dadantii

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

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

B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B 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
GTP
Query on GTP
B NON-POLYMER C10 H16 N5 O14 P3 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.192
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 67.44 α = 90.00
b = 78.37 β = 90.00
c = 98.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-12-02
  • Released Date: 2017-02-01
  • Deposition author(s): Battaglia, R.A., Price, I.R., Ke, A.

Revision History

  • Version 1_0: 2017-02-01

    Type: Initial release

  • Version 1_1: 2017-02-15

    Type: Database references

  • Version 1_2: 2017-03-29

    Type: Database references

  • Version 1_3: 2017-09-27

    Type: Author supporting evidence