4Q9R

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 4Q9R

Classification: RNA / immune system

Total Structure Weight: 74679.73


Macromolecule Entities
Molecule Chains Length Organism Details
Fab BL3-6, HEAVY CHAIN H 223 Mus musculus
Fab BL3-6, LIGHT CHAIN L 214 Mus musculus
Macromolecule Entities
Molecule Chains Length Organism Details
Spinach RNA aptamer R 84 Synthetic construct

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

R (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)- 2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro- 4H-imidazol-4-one
C13 H9 F5 N2 O2
AWYCLBWNRONMQC-WMZJFQQLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

R POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
GDP
Query on GDP
R RNA LINKING C10 H15 N5 O11 P2 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.203
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 147.51 α = 90.00
b = 78.99 β = 112.42
c = 94.36 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-05-01
  • Released Date: 2014-06-18
  • Deposition author(s): Huang, H., Suslov, N.B., Li, N.-S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Revision History

  • Version 1_0: 2014-06-18

    Type: Initial release

  • Version 1_1: 2014-07-09

    Type: Database references

  • Version 1_2: 2014-07-30

    Type: Database references

  • Version 1_3: 2014-10-15

    Type: Structure summary

  • Version 2_0: 2017-07-26

    Type: Advisory, Atomic model, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary