1F06

THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE

Structural Biology Knowledgebase: 1F06 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 1F06

Classification: OXIDOREDUCTASE

Total Structure Weight: 72163.34

Macromolecule Entities
Molecule Chains Length Organism Details
MESO-DIAMINOPIMELATE D-DEHYDROGENASE A, B 320 Corynebacterium glutamicum EC#: 1.4.1.16 IUBMB
Gene Name(s): ddh Cgl2617 cg2900
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2NP
Query on 2NP

B L-2-AMINO-6-METHYLENE-PIMELIC ACID
C8 H13 N O4
SGAIRWMSXVAPOO-LURJTMIESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2NP N/A in BindingDB
Ki: 5000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.179
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.55 α = 90.00
b = 65.59 β = 106.52
c = 84.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-05-14
  • Released Date: 2001-05-14
  • Deposition author(s): Cirilli, M., Scapin, G., Sutherland, A., Caplan, J.F., Vederas, J.C., Blanchard, J.S.

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