1M0N

Structure of Dialkylglycine Decarboxylase Complexed with 1-Aminocyclopentanephosphonate

Structural Biology Knowledgebase: 1M0N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 1M0N

Classification: LYASE

Total Structure Weight: 47034.23

Macromolecule Entities
Molecule Chains Length Organism Details
2,2-Dialkylglycine decarboxylase A 433 Burkholderia cepacia EC#: 4.1.1.64 IUBMB
Mutation: Q15H, G81E
Gene Name(s): dgdA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN- 4-YL}METHYLENE)AMINO]CYCLOPENTYLPHOSPHONIC ACID
C13 H20 N2 O8 P2
NPYNJFSRGFRPCR-VIZOYTHASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HCP N/A in BindingDB
Ki: 6000000 nM  BindingMOAD
Ki: 6000000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.189
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 151.29 α = 90.00
b = 151.29 β = 90.00
c = 84.79 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-13
  • Released Date: 2002-10-23
  • Deposition author(s): Liu, W., Rogers, C.J., Fisher, A.J., Toney, M.D.

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