5V3F

Co-crystal structure of the fluorogenic RNA Mango


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 5V3F

Classification: RNA

Total Structure Weight: 22428.93

Macromolecule Entities
Molecule Chains Length Organism Details
RNA (31-MER) A, B 31 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
74G
Query on 74G

A, B 4-{[(2S)-3-{2,16-dioxo-20-[(3aS,4S,6aR)-2- oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]- 6,9,12-trioxa-3,15-diazaicosan-1-yl}-2,3- dihydro-1,3-benzothiazol-2-yl]methyl}-1-methylquinolin- 1-ium
C38 H51 N6 O6 S2
BXBHTLUUPXOIJA-SDUHKGLLSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.196
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 63.20 α = 90.00
b = 63.20 β = 90.00
c = 138.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-07
  • Released Date: 2017-05-24
  • Deposition author(s): Trachman, R.J., Ferre-D'Amare, A.R.

Revision History

  • Version 1_0: 2017-05-24

    Type: Initial release

  • Version 1_1: 2017-06-14

    Type: Database references

  • Version 1_2: 2017-06-28

    Type: Database references