4GBJ

Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans

Structural Biology Knowledgebase: 4GBJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 4GBJ

Classification: OXIDOREDUCTASE

Total Structure Weight: 128774.49

Macromolecule Entities
Molecule Chains Length Organism Details
6-phosphogluconate dehydrogenase NAD-binding A, B, C, D 297 Dyadobacter fermentans Gene Name(s): Dfer_3638
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NA
Query on NA

B, C, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 79.63 α = 90.00
b = 89.64 β = 90.00
c = 151.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-27
  • Released Date: 2012-09-05
  • Deposition author(s): Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release