1MDX

Crystal structure of ArnB transferase with pyridoxal 5' phosphate

Structural Biology Knowledgebase: 1MDX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1MDX

Classification: TRANSFERASE

Total Structure Weight: 43409.63

Macromolecule Entities
Molecule Chains Length Organism Details
ArnB aminotransferase A 393 Salmonella enterica EC#: 2.6.1.87 IUBMB
Gene Name(s): arnB pbgP pbgP1 pmrH STM2297
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AKG
Query on AKG

A 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.198
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.15 α = 90.00
b = 91.15 β = 90.00
c = 128.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-07
  • Released Date: 2002-12-11
  • Deposition author(s): Noland, B.W., Newman, J.M., Hendle, J., Badger, J., Christopher, J.A., Tresser, J., Buchanan, M.D., Wright, T.A., Rutter, M.E., Sanderson, W.E., Muller-Dieckmann, H.-J., Gajiwala, K.S., Buchanan, S.G.

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