3H7K

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase Complexed with a Covalently Bound Reaction Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.147

Literature

Macromolecules
Sequence Display for 3H7K

Classification: HYDROLASE

Total Structure Weight: 43983.49

Macromolecule Entities
Molecule Chains Length Organism Details
Agmatine deiminase A 383 Arabidopsis thaliana EC#: 3.5.3.12 IUBMB
Mutation: D49G
Gene Name(s): AIH EMB1873 At5g08170 T22D6.110
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET
AGT
Query on AGT
A L-PEPTIDE LINKING C8 H20 N4 O2 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.185
  • R-Value Work: 0.147
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 123.72 α = 90.00
b = 69.56 β = 98.52
c = 50.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-04-27
  • Released Date: 2009-05-26
  • Deposition author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2011-08-10
    Type: Non-polymer description
  • 2011-08-17
    Type: Structure summary