1M83

Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in a Closed, Pre-transition State Conformation

Structural Biology Knowledgebase: 1M83 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 1M83

Classification: LIGASE

Total Structure Weight: 38033.72

Macromolecule Entities
Molecule Chains Length Organism Details
Tryptophan-tRNA ligase A 328 Geobacillus stearothermophilus EC#: 6.1.1.2 IUBMB
Gene Name(s): trpS
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ATP N/A in BindingDB
Kd: 400000 nM  BindingMOAD
Kd: 400000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.210
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.13 α = 90.00
b = 62.13 β = 90.00
c = 217.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-24
  • Released Date: 2002-12-18
  • Deposition author(s): Retailleau, P., Huang, X., Yin, Y., Hu, M., Weinreb, V., Vachette, P., Vonrhein, C., Bricogne, G., Roversi, P., Ilyin, V., Carter Jr., C.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values