1IK3

LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structure of a purple lipoxygenase.

Skrzypczak-Jankun, E.Bross, R.A.Carroll, R.T.Dunham, W.R.Funk, M.O.

(2001) J Am Chem Soc 123: 10814-10820

  • DOI: 10.1021/ja011759t
  • Primary Citation of Related Structures:  
    1IK3

  • PubMed Abstract: 
  • Polyunsaturated fatty acid metabolism is governed primarily by two enzymes, prostaglandin H synthase and lipoxygenase. The crystal structure of the metastable product-oxidized purple form of soybean lipoxygenase-3 was determined at 2.0 A resolution. The data reveal that the chromophore corresponds to an iron-peroxide complex, a potential intermediate in the catalyzed reaction ...

    Polyunsaturated fatty acid metabolism is governed primarily by two enzymes, prostaglandin H synthase and lipoxygenase. The crystal structure of the metastable product-oxidized purple form of soybean lipoxygenase-3 was determined at 2.0 A resolution. The data reveal that the chromophore corresponds to an iron-peroxide complex, a potential intermediate in the catalyzed reaction. A significant alteration of the iron site accompanies the formation of the complex. The structure, the first for a fatty acid-lipoxygenase complex, also reveals an unexpected mode of binding, and identifies amino acid residues that may play significant roles in catalysis, regio- and stereoselectivity.


    Related Citations: 
    • Structure of Soybean Lipoxygenase L3 and a Comparison with its L1 Isoenzyme
      Skrzypczak-Jankun, E., Amzel, L.M., Kroa, B.A., Funk Jr., M.O.
      (1997) Proteins 29: 15
    • Structural and Thermochemical Characterization of Lipoxygenase-Catechol Complexes
      Pham, C., Jankun, J., Skrzypczak-Jankun, E., Flowers II, R.A., Funk Jr., M.O.
      (1998) Biochemistry 37: 17952
    • Curcumin Inhibits Lipoxygenase by Binding to its Central Cavity: Theoretical and X-Ray Evidence.
      Skrzypczak-Jankun, E., Mccabe, N.P., Selman, S.H., Jankun, J.
      (2000) Int J Mol Med 6: 521

    Organizational Affiliation

    Department of Chemistry, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA. ejankun@protein.wo.utoledo.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIPOXYGENASE-3A857Glycine maxMutation(s): 0 
Gene Names: LOX1.3LOX3
EC: 1.13.11.12 (PDB Primary Data), 1.13.11.58 (UniProt)
UniProt
Find proteins for P09186 (Glycine max)
Explore P09186 
Go to UniProtKB:  P09186
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
11O (Subject of Investigation/LOI)
Query on 11O

Download Ideal Coordinates CCD File 
F [auth A](TRANS-12,13-EPOXY)-11-HYDROXY-9(Z)-OCTADECENOIC ACID
C18 H32 O4
UZCLYICSWADYGM-RXWDXHPSSA-N
 Ligand Interaction
9OH (Subject of Investigation/LOI)
Query on 9OH

Download Ideal Coordinates CCD File 
E [auth A](TRANS-12,13-EPOXY)-9-HYDROXY-10(E)-OCTADECENOIC ACID
C18 H32 O4
WCCLYKMJXGYGEN-WFZKJPOOSA-N
 Ligand Interaction
13R (Subject of Investigation/LOI)
Query on 13R

Download Ideal Coordinates CCD File 
D [auth A]13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
C18 H32 O4
JDSRHVWSAMTSSN-PIHGWCCBSA-N
 Ligand Interaction
13S (Subject of Investigation/LOI)
Query on 13S

Download Ideal Coordinates CCD File 
C [auth A]13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
C18 H32 O4
JDSRHVWSAMTSSN-IRQZEAMPSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.65α = 90
b = 137.28β = 95.56
c = 61.89γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description