3K5T

Crystal structure of human diamine oxidase in space group C2221

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

A new crystal form of human diamine oxidase.

McGrath, A.P., Hilmer, K.M., Collyer, C.A., Dooley, D.M., Guss, J.M.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 137-142

  • DOI: https://doi.org/10.1107/S1744309109052130
  • Primary Citation of Related Structures:  
    3K5T

  • PubMed Abstract: 

    Copper amine oxidases (CAOs) are ubiquitous in nature and catalyse the oxidative deamination of primary amines to the corresponding aldehydes. Humans have three viable CAO genes (AOC1-3). AOC1 encodes human diamine oxidase (hDAO), which is the frontline enzyme for histamine metabolism. hDAO is unique among CAOs in that it has a distinct substrate preference for diamines. The structure of hDAO in space group P2(1)2(1)2(1) with two molecules in the asymmetric unit has recently been reported. Here, the structure of hDAO refined to 2.1 A resolution in space group C222(1) with one molecule in the asymmetric unit is reported.

    • Organizational Affiliation: 

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia. a.mcgrath@mmb.usyd.edu.au


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diamine oxidase731Homo sapiensMutation(s): 3 
Gene Names: ABP1, AOC1, DAO1
EC: 1.4.3.22
UniProt & NIH Common Fund Data Resources
Find proteins for P19801 (Homo sapiens)
Explore P19801 
Go to UniProtKB:  P19801
PHAROS:  P19801
GTEx:  ENSG00000002726 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19801
Glycosylation
Glycosylation Sites: 3
Go to GlyGen: P19801-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPQ
Query on TPQ
A
L-PEPTIDE LINKINGC9 H9 N O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.771α = 90
b = 96.954β = 90
c = 178.06γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-13
    Changes: Database references, Structure summary
  • Version 2.2: 2023-09-06
    Changes: Data collection, Refinement description