1KOG

Crystal structure of E. coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator

Structural Biology Knowledgebase: 1KOG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.251

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KOG

Classification: LIGASE / RNA

Total Structure Weight: 472579.78


Macromolecule Entities
Molecule Chains Length Organism Details
Threonyl-tRNA synthetase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 401 Escherichia coli EC#: 6.1.1.3 IUBMB
Fragment: Catalytic and anticodon binding domains (residues 242 to 642)
Gene Name(s): thrS b1719 JW1709
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
Threonyl-tRNA synthetase mRNA I, J, K... , L, M, N, O, P I, J, K, L, M, N, O, P 37 synthetic Domain D2 of the trs mRNA operator from E.coli (nucleotides -49 to -13)

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

A, B, C, D, E, F, G, H 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
C14 H21 N7 O8 S
UPVAPSGKXAAHBG-CKTDUXNWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F, G, H ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.251
  • Space Group: P 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 188.45 α = 90.00
b = 101.74 β = 114.40
c = 199.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-20
  • Released Date: 2002-04-26
  • Deposition author(s): Torres-Larrios, A., Dock-Bregeon, A.C., Romby, P., Rees, B., Sankaranarayanan, R., Caillet, J., Springer, M., Ehresmann, C., Ehresmann, B., Moras, D.

Revision History

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