1JQ3

Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO

Structural Biology Knowledgebase: 1JQ3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1JQ3

Classification: TRANSFERASE

Total Structure Weight: 138007.89

Macromolecule Entities
Molecule Chains Length Organism Details
Spermidine synthase A, B, C, D 296 Thermotoga maritima EC#: 2.5.1.16 IUBMB
Gene Name(s): speE TM_0654
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AAT
Query on AAT

A, C, D S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE
C18 H29 N7 O3 S
SUUGLGYBZXSJAA-SCFUHWHPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AAT N/A in BindingDB
IC50: 200 nM  BindingMOAD
IC50: 200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.196
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 132.52 α = 90.00
b = 198.02 β = 90.00
c = 51.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-08-03
  • Released Date: 2001-11-21
  • Deposition author(s): Korolev, S., Ikeguchi, Y., Skarina, T., Beasley, S., Edwards, A., Joachimiak, A., Pegg, A.E., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History

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