3ZYV | pdb_00003zyv

Crystal structure of the mouse liver Aldehyde Oxidase 3 (mAOX3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 
    0.285 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The First Mammalian Aldehyde Oxidase Crystal Structure: Insights Into Substrate Specificity.

Coelho, C.Mahro, M.Trincao, J.Carvalho, A.T.P.Ramos, M.J.Terao, M.Garattini, E.Leimkuhler, S.Romao, M.J.

(2012) J Biological Chem 287: 40690

  • DOI: https://doi.org/10.1074/jbc.M112.390419
  • Primary Citation Related Structures: 
    3ZYV

  • PubMed Abstract: 

    Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.


  • Organizational Affiliation
    • Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.

Macromolecule Content 

  • Total Structure Weight: 595.23 kDa 
  • Atom Count: 38,315 
  • Modeled Residue Count: 5,016 
  • Deposited Residue Count: 5,340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AOX3
A, B, C, D
1,335Mus musculusMutation(s): 0 
EC: 1.2.3.1 (PDB Primary Data), 1.17.3 (UniProt)
UniProt
Find proteins for G3X982 (Mus musculus)
Explore G3X982 
Go to UniProtKB:  G3X982
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3X982
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
BA [auth D],
J [auth A],
P [auth B],
V [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE

Query on MTE



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B],
T [auth C],
Z [auth D]
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
L [auth B]
M [auth B]
R [auth C]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C],
X [auth D],
Y [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS

Query on MOS



Download:Ideal Coordinates CCD File
AA [auth D],
I [auth A],
O [auth B],
U [auth C]
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
Q [auth C],
W [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.88α = 78.16
b = 135.27β = 77.72
c = 147.37γ = 89.9
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2013-04-24
    Changes: Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description