1MDZ

Crystal structure of ArnB aminotransferase with cycloserine and pyridoxal 5' phosphate

Structural Biology Knowledgebase: 1MDZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.212

Literature

Macromolecules
Sequence Display for 1MDZ

Classification: TRANSFERASE

Total Structure Weight: 43412.59

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 2 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)
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.212
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.90 α = 90.00
b = 90.90 β = 90.00
c = 127.71 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., Rutter, M.E., Sanderson, W.E., Muller-Dieckmann, H.-J., Gajiwala, K.S., Buchanan, S.G.

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