3PD4

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with glycyl-3'-aminoadenosine

Structural Biology Knowledgebase: 3PD4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PD4

Classification: LIGASE

Total Structure Weight: 34123.53

Macromolecule Entities
Molecule Chains Length Organism Details
Threonyl-tRNA synthetase A, B 147 Pyrococcus abyssi EC#: 6.1.1.3 IUBMB
Fragment: UNP RESIDUES 1-147
Gene Name(s): thrS PYRAB13430 PAB1490

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A3G
Query on A3G

A, B 3'-deoxy-3'-(glycylamino)adenosine
C12 H17 N7 O4
XJJYXFHVLHMVGL-MUIQIWNUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
A3G N/A in BindingDB
Kd: 33300 nM  BindingMOAD
Kd: 33200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.204
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.33 α = 90.00
b = 69.08 β = 90.00
c = 94.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-22
  • Released Date: 2010-12-08
  • Deposition author(s): Hussain, T., Kamarthapu, V., Kruparani, S.P., Sankaranarayanan, R.

Revision History

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