1RK8

Structure of the cytosolic protein PYM bound to the Mago-Y14 core of the exon junction complex

Structural Biology Knowledgebase: 1RK8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.235

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RK8

Classification: TRANSLATION

Total Structure Weight: 43108.01

Macromolecule Entities
Molecule Chains Length Organism Details
CG8781-PA protein A 165 Drosophila melanogaster Fragment: RBD domain
Gene Name(s): tsu Y14 CG8781
Mago nashi protein B 147 Drosophila melanogaster Fragment: full-length
Gene Name(s): mago mgn CG9401
Within the bgcn gene intron protein C 58 Drosophila melanogaster Fragment: N-terminal domain (residues 1-58)
Gene Name(s): Pym wibg CG30176

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.235
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 106.36 α = 90.00
b = 106.36 β = 90.00
c = 58.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-11-21
  • Released Date: 2004-04-13
  • Deposition author(s): Bono, F., Ebert, J., Guettler, T., Izaurralde, E., Conti, E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4