1W5Z

AGAO covalent complex with Benzylhydrazine

• PDB DOI: https://doi.org/10.2210/pdb1W5Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arthrobacter globiformis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-11 Released: 2005-12-08 
• Deposition Author(s): Duff, A.P., Trambaiolo, D.M., Langley, D.B., Juda, G.A., Shepard, E.M., Dooley, D.M., Freeman, H.C., Guss, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.187 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Literature

Complexes of the Copper-Containing Amine Oxidase from Arthrobacter Globiformis with the Inhibitors Benzylhydrazine and Tranylcypromine.

Langley, D.B., Trambaiolo, D.M., Duff, A.P., Dooley, D.M., Freeman, H.C., Guss, J.M.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 577

• PubMed: 18607080 
• DOI: https://doi.org/10.1107/S174430910801556X
• Primary Citation of Related Structures:  
  1W4N, 1W5Z


• PubMed Abstract: 
  

  Complexes of Arthrobacter globiformis amine oxidase (AGAO) with the inhibitors benzylhydrazine and tranylcypromine (an antidepressant drug) have been refined at 1.86 and 1.65 A resolution, respectively. Both inhibitors form covalent adducts with the TPQ cofactor. A tyrosine residue, proposed to act as a gate to the AGAO active site, is in its open conformation.

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Organizational Affiliation: 

School of Molecular and Microbial Biosciences, University of Sydney, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 72.7 kDa 
• Atom Count: 5,431 
• Modelled Residue Count: 621 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENYLETHYLAMINE OXIDASE	A	646	Arthrobacter globiformis	Mutation(s): 0  EC: 1.4.3.6
UniProt
Find proteins for P46881 (Arthrobacter globiformis) Explore P46881  Go to UniProtKB:  P46881

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.187 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.126	α = 90
b = 62.665	β = 112.07
c = 92.283	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-08 
Deposition Author(s): Duff, A.P., Trambaiolo, D.M., Langley, D.B., Juda, G.A., Shepard, E.M., Dooley, D.M., Freeman, H.C., Guss, J.M.

Revision History  

• Version 1.0: 2005-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2013-08-07
  Changes: Non-polymer description, Other, Source and taxonomy
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other
• Version 2.1: 2023-12-13
  Changes: Refinement description