1D7U

Crystal structure of the complex of 2,2-dialkylglycine decarboxylase with LCS

Structural Biology Knowledgebase: 1D7U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1D7U

Classification: LYASE

Total Structure Weight: 46889.11

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)) A 433 Burkholderia cepacia EC#: 4.1.1.64 IUBMB
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
LCS
Query on LCS

A [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin- 4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate
C11 H14 N3 O7 P
KFCQHWOGBVCKHR-UKTHLTGXSA-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: 1.95 Å
  • R-Value Observed:
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 153.23 α = 90.00
b = 153.23 β = 90.00
c = 86.48 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-19
  • Released Date: 1999-11-19
  • Deposition author(s): Malashkevich, V.N., Toney, M.D., Strop, P., Keller, J., Jansonius, J.N.

Revision History

  • 2011-08-24
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4