3PD2

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

Structural Biology Knowledgebase: 3PD2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PD2

Classification: LIGASE

Total Structure Weight: 34183.59

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
A3S
Query on A3S

A, B SERINE-3'-AMINOADENOSINE
N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE (Synonym)
C13 H19 N7 O5
ITDKSTILAWHDJI-AYEBZEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
A3S N/A in BindingDB
Kd: 3400 nM  BindingMOAD
Kd: 3400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.195
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 37.23 α = 90.00
b = 66.33 β = 90.00
c = 93.18 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

  • 2014-03-05
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4