1W5Z | pdb_00001w5z

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.187 (Depositor), 0.192 (DCC)
R-Value Work:
0.152 (Depositor), 0.159 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S174430910801556X
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENYLETHYLAMINE OXIDASE	A	646	Arthrobacter globiformis	Mutation(s): 0 EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P46881 (Arthrobacter globiformis) Explore P46881 Go to UniProtKB: P46881
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3TY Query on 3TY	A	L-PEPTIDE LINKING	C₁₆ H₁₇ N₃ O₄		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.187 (Depositor), 0.192 (DCC)
R-Value Work: 0.152 (Depositor), 0.159 (DCC)
R-Value Observed: 0.154 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2005-12-08

Deposition Author(s):

Revision History (Full details and data files)

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
Version 3.0: 2025-07-30
Changes: Polymer sequence, Structure summary