4P5J

Crystal structure of the tRNA-like structure from Turnip Yellow Mosaic Virus (TYMV), a tRNA mimicking RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 4P5J

Classification: RNA

Total Structure Weight: 31377.07

Macromolecule Entities
Molecule Chains Length Organism Details
Turnip yellow mosaic virus mRNA for the coat protein A 86 Turnip yellow mosaic virus

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

A IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SPM
Query on SPM

A SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-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 1 Unique
ID Chains Type Formula 2D Diagram Parent
A23
Query on A23
A RNA LINKING C10 H13 N5 O9 P2 A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.206
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 55.27 α = 90.00
b = 101.57 β = 90.00
c = 111.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-03-17
  • Released Date: 2014-06-04
  • Deposition author(s): Colussi, T.M., Costantino, D.A., Hammond, J.A., Ruehle, G.M., Nix, J.C., Kieft, J.S.

Revision History

  • Version 1_0: 2014-06-04

    Type: Initial release

  • Version 1_1: 2014-06-25

    Type: Database references

  • Version 1_2: 2014-07-30

    Type: Database references

  • Version 1_3: 2014-10-01

    Type: Database references

  • Version 1_4: 2017-09-06

    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy