1D7S

CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH DCS

Structural Biology Knowledgebase: 1D7S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Work: 0.186

Currently 1D7S does not have a wwPDB validation report.


Literature

Macromolecules
Sequence Display for 1D7S

Classification: LYASE

Total Structure Weight: 46891.13

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
DCS
Query on DCS

A D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE (Synonym)
C11 H16 N3 O7 P
NNRZSZJOQKAGTO-SECBINFHSA-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: 2.05 Å
  • R-Value Observed:
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 152.88 α = 90.00
b = 152.88 β = 90.00
c = 86.36 γ = 120.00

Structure Validation

Currently 1D7S does not have a validation report.



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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values