5BJO

Crystal structure of the Corn RNA aptamer in complex with DFHO, site-specific 5-iodo-U


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 5BJO

Classification: RNA

Total Structure Weight: 24374.82

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (36-MER) E, Y 36 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
747
Query on 747

Y (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]- 2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5- dihydro-4H-imidazol-4-one
C12 H9 F2 N3 O3
MZFHSQVSFUWKDU-TUUOAFJKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

E, Y 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
IU
Query on IU
E, Y RNA LINKING C9 H12 I N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.180
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 36.27 α = 90.00
b = 55.31 β = 90.00
c = 99.00 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-08-21
  • Released Date: 2017-09-27
  • Deposition author(s): Warner, K.D., Song, W., Filonov, G.S., Jaffrey, S.R., Ferre-D'Amare, A.R.

Revision History

  • Version 1_0: 2017-09-27

    Type: Initial release

  • Version 1_1: 2017-10-11

    Type: Database references

  • Version 1_2: 2017-10-25

    Type: Database references