1NO3

REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT 2.15 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Soybean lipoxygenase-3 in complex with 4-nitrocatechol.

Skrzypczak-Jankun, E.Borbulevych, O.Y.Jankun, J.

(2004) Acta Crystallogr.,Sect.D 60: 613-615

  • DOI: 10.1107/S0907444904000861

  • PubMed Abstract: 
  • 4-Nitrocatechol (4NC) is a known inhibitor of lipoxygenase. This work presents the X-ray structure of soybean lipoxygenase-3 in complex with 4NC refined at 2.15 A resolution. The X-ray analysis shows 4NC near iron with partial occupancy, blocking acc ...

    4-Nitrocatechol (4NC) is a known inhibitor of lipoxygenase. This work presents the X-ray structure of soybean lipoxygenase-3 in complex with 4NC refined at 2.15 A resolution. The X-ray analysis shows 4NC near iron with partial occupancy, blocking access to Fe but not covalently bound to it. The two hydroxyl groups interact with the C-terminus (4-OH) and His523 ND1 (3-OH). The residues surrounding the iron cofactor, His518*, His523, His709, Ile857* COO(-) and water, form a trigonal bipyramid with the residues marked with asterisks in the axial positions. The water bound to iron and the presence of the inhibitor seem to be responsible for the rearrangements and changes in the geometry of the ligand distribution and confirm the displacement of His518 from iron coordination. A description of the catechol binding contributes to the understanding of lipoxygenase inhibition and the participation of its co-oxidative activity in the utilization of natural flavonoids.


    Related Citations: 
    • Structural and thermochemical characterization of Lipoxygenase-catechol complexes
      Pham, C.,Jankun, J.,Skrzypczak-Jankun, E.,Flowers, R.A.,Funk Jr., M.O.
      (1998) Biochemistry 37: 17952


    Organizational Affiliation

    Medical College of Ohio, Urology Research Center, Department of Urology, 3065 Arlington Avenue, Toledo OH 43614, USA. eskrzypczak@mco.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoxygenase-3
A
857Glycine maxGene Names: LOX1.3 (LOX3)
EC: 1.13.11.58
Find proteins for P09186 (Glycine max)
Go to UniProtKB:  P09186
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NC
Query on 4NC

Download SDF File 
Download CCD File 
A
4-NITROCATECHOL
C6 H5 N O4
XJNPNXSISMKQEX-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.905α = 90.00
b = 137.531β = 95.48
c = 61.880γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description