4QK8

Thermoanaerobacter pseudethanolicus c-di-AMP riboswitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 4QK8

Classification: RNA

Total Structure Weight: 41271.66

Macromolecule Entities
Molecule Chains Length Organism Details
C-di-AMP riboswitch A 122 synthetic

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

A (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9- bis(6-amino-9H-purin-9-yl)octahydro-2H,7H- difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine- 3,5,10,12-tetrol 5,12-dioxide
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate (Synonym)
C20 H24 N10 O12 P2
PDXMFTWFFKBFIN-XPWFQUROSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A POTASSIUM ION
K
NPYPAHLBTDXSSS-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)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
A NON-POLYMER C10 H16 N5 O14 P3 G
23G
Query on 23G
A RNA OH 3 prime terminus C10 H13 N5 O10 P2 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.181
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 114.87 α = 90.00
b = 114.87 β = 90.00
c = 114.71 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-06-05
  • Released Date: 2014-08-06
  • Deposition author(s): Gao, A., Serganov, A.

Revision History

  • Version 1_0: 2014-08-06

    Type: Initial release

  • Version 1_1: 2014-08-27

    Type: Database references

  • Version 1_2: 2014-09-10

    Type: Database references