3PD5

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of threonyl-adenylate

Structural Biology Knowledgebase: 3PD5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PD5

Classification: LIGASE

Total Structure Weight: 34463.94

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 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TSB
Query on TSB

A, B 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
C14 H21 N7 O8 S
UPVAPSGKXAAHBG-CKTDUXNWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.291
  • R-Value Work: 0.222
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.47 α = 90.00
b = 72.09 β = 90.00
c = 96.56 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