3RDE

Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of 12-lipoxygenase catalytic-domain-inhibitor complex identifies a substrate-binding channel for catalysis.

Xu, S., Mueser, T.C., Marnett, L.J., Funk, M.O.

(2012) Structure 20: 1490-1497

  • DOI: 10.1016/j.str.2012.06.003

  • PubMed Abstract: 

    • Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and ...

    Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and cancer. Crystals diffracting to high resolution (1.9 Å) were obtained for a complex between the catalytic domain of leukocyte 12-lipoxygenase and the isoform-specific inhibitor, 4-(2-oxapentadeca-4-yne)phenylpropanoic acid (OPP). In the three-dimensional structure of the complex, the inhibitor occupied a new U-shaped channel open at one end to the surface of the protein and extending past the redox-active iron site that is essential for catalysis. In models, the channel accommodated arachidonic acid, defining the binding site for the substrate of the catalyzed reaction. There was a void adjacent to the OPP binding site connecting to the surface of the enzyme and providing a plausible access channel for the other substrate, oxygen.

    Organizational Affiliation: 

    Department of Chemistry, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arachidonate 12-lipoxygenase, 12S-type
A, B, C, D
573Sus scrofaMutation(s): 3 
Gene Names: ALOX15
EC: 1.13.11.33
Find proteins for P16469 (Sus scrofa)
Go to Gene View: ALOX15
Go to UniProtKB:  P16469
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
A, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
OYP
Query on OYP
Download SDF File 
Download CCD File 
A, B, C, D
3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid
C23 H34 O3
RYRHYCDBTFUGMI-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2
Download SDF File 
Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OYPIC50: 35 nM (99) BINDINGDB
OYPIC50: 35 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.450α = 90.00
b = 181.540β = 92.86
c = 91.610γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
HKL-2000data collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-06-20
    Type: Database references
  • Version 1.2: 2012-08-01
    Type: Database references
  • Version 1.3: 2012-09-26
    Type: Database references