1DKA

DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES

Structural Biology Knowledgebase: 1DKA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Observed: 0.176

Literature

Macromolecules
Sequence Display for 1DKA

Classification: LYASE(DECARBOXYLASE)

Total Structure Weight: 47082.35

Macromolecule Entities
Molecule Chains Length Organism Details
2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE) 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 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Observed: 0.176
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 152.70 α = 90.00
b = 152.70 β = 90.00
c = 86.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-06-18
  • Released Date: 1994-10-15
  • Deposition author(s): Toney, M.D., Hohenester, E., Jansonius, J.N.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update