Short chain specific acyl-CoA oxidase from Arabidopsis thaliana, ACX4 in complex with acetoacetyl-CoA

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Controlling Electron Transfer in Acyl-Coa Oxidases and Dehydrogenases: A Structural View.

Mackenzie, J.Pedersen, L.Arent, S.Henriksen, A.

(2006) J Biol Chem 281: 31012

  • DOI: https://doi.org/10.1074/jbc.M603405200
  • Primary Citation of Related Structures:  
    2IX5, 2IX6

  • PubMed Abstract: 

    Plants produce a unique peroxisomal short chain-specific acyl-CoA oxidase (ACX4) for beta-oxidation of lipids. The short chain-specific oxidase has little resemblance to other peroxisomal acyl-CoA oxidases but has an approximately 30% sequence identity to mitochondrial acyl-CoA dehydrogenases. Two biochemical features have been linked to structural properties by comparing the structures of short chain-specific Arabidopsis thaliana ACX4 with and without a substrate analogue bound in the active site to known acyl-CoA oxidases and dehydrogenase structures: (i) a solvent-accessible acyl binding pocket is not required for oxygen reactivity, and (ii) the oligomeric state plays a role in substrate pocket architecture but is not linked to oxygen reactivity. The structures indicate that the acyl-CoA oxidases may encapsulate the electrons for transfer to molecular oxygen by blocking the dehydrogenase substrate interaction site with structural extensions. A small binding pocket observed adjoining the flavin adenine dinucleotide N5 and C4a atoms could increase the number of productive encounters between flavin adenine dinucleotide and O2.

  • Organizational Affiliation

    Biostructure Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
436Arabidopsis thalianaMutation(s): 0 
Find proteins for Q96329 (Arabidopsis thaliana)
Explore Q96329 
Go to UniProtKB:  Q96329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96329
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.747α = 90
b = 144.747β = 90
c = 149.208γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description