3EPJ

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

Structural Biology Knowledgebase: 3EPJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 3EPJ

Classification: Transferase / RNA

Total Structure Weight: 141367.13


Macromolecule Entities
Molecule Chains Length Organism Details
tRNA isopentenyltransferase A, B 409 Saccharomyces cerevisiae EC#: 2.5.1.75 IUBMB
Fragment: UNP residues 13-421
Gene Name(s): MOD5 YOR274W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
tRNA E, F 69 synthetic

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

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, E, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.198
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 162.92 α = 90.00
b = 211.03 β = 90.00
c = 126.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-29
  • Released Date: 2008-11-04
  • Deposition author(s): Huang, R.H., Zhou, C.

Revision History

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