1DJ9

CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.

Structural Biology Knowledgebase: 1DJ9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.212

Literature

Macromolecules
Sequence Display for 1DJ9

Classification: TRANSFERASE

Total Structure Weight: 42174.25

Macromolecule Entities
Molecule Chains Length Organism Details
8-AMINO-7-OXONONANOATE SYNTHASE A 384 Escherichia coli EC#: 2.3.1.47 IUBMB
Gene Name(s): bioF b0776 JW0759
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY- 2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL- METHANE]
N-PYRIDOXYL-7-KETO-8-AMINOPELARGONIC ACID- 5'-MONOPHOSPHATE (Synonym)
C17 H27 N2 O8 P
YXEXNGWPUWJMIT-NSHDSACASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.212
  • Space Group: P 31 1 2

Unit Cell:

Length (Å) Angle (°)
a = 58.89 α = 90.00
b = 58.89 β = 90.00
c = 201.77 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-12-02
  • Released Date: 2000-12-06
  • Deposition author(s): Webster, S.P., Alexeev, D., Campopiano, D.J., Watt, R.M., Alexeeva, M., Sawyer, L., Baxter, R.L.

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