1D7V

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

Structural Biology Knowledgebase: 1D7V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 1D7V

Classification: LYASE

Total Structure Weight: 46892.16

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
NMA
Query on NMA

A N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4-YLMETHYL]-2-METHYLALANINE
N-PYRIDOXYL-2-METHYLALANINE-5-PHOSPHATE (Synonym)
C12 H19 N2 O7 P
NHGDGJKONAZETF-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: 2.8 Å
  • R-Value Observed:
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 153.20 α = 90.00
b = 153.20 β = 90.00
c = 86.90 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

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