1WYD

Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 1WYD

Classification: LIGASE

Total Structure Weight: 99027.37

Macromolecule Entities
Molecule Chains Length Organism Details
hypothetical aspartyl-tRNA synthetase A, B 429 Sulfolobus tokodaii Gene Name(s): aspS STK_02050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.232
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 116.30 α = 90.00
b = 139.25 β = 90.00
c = 75.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-12
  • Released Date: 2006-07-04
  • Deposition author(s): Maeda, Y., Hossain, M.T., Ubukata, S., Suzuki, K., Sekiguchi, T., Takenaka, A.

Revision History

  • Version 1_0: 2006-07-04

    Type: Initial release

  • Version 1_1: 2007-09-14

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Source and taxonomy, Version format compliance