1IK3 | pdb_00001ik3

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

• PDB DOI: https://doi.org/10.2210/pdb1IK3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Glycine max
• Mutation(s): No 


• Deposited: 2001-05-01 Released: 2001-11-14 
• Deposition Author(s): Skrzypczak-Jankun, E., Funk Jr., M.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.296 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 11686682 
• DOI: https://doi.org/10.1021/ja011759t
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 98.22 kDa 
• Atom Count: 7,314 
• Modeled Residue Count: 836 
• Deposited Residue Count: 857 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPOXYGENASE-3	A	857	Glycine max	Mutation(s): 0  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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
11O	F [auth A]	(TRANS-12,13-EPOXY)-11-HYDROXY-9(Z)-OCTADECENOIC ACID C18 H32 O4 UZCLYICSWADYGM-RXWDXHPSSA-N
9OH	E [auth A]	(TRANS-12,13-EPOXY)-9-HYDROXY-10(E)-OCTADECENOIC ACID C18 H32 O4 WCCLYKMJXGYGEN-WFZKJPOOSA-N
13R	D [auth A]	13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID C18 H32 O4 JDSRHVWSAMTSSN-PIHGWCCBSA-N
13S	C [auth A]	13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID C18 H32 O4 JDSRHVWSAMTSSN-IRQZEAMPSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.296 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.65	α = 90
b = 137.28	β = 95.56
c = 61.89	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-14 
Deposition Author(s): Skrzypczak-Jankun, E., Funk Jr., M.O.

Revision History  

• 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
• Version 1.4: 2023-08-16
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary