1LVN | pdb_00001lvn

CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE COMPLEXED WITH TRANYLCYPROMINE

• PDB DOI: https://doi.org/10.2210/pdb1LVN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-05-28 Released: 2003-08-05 
• Deposition Author(s): Wilmot, C.M., Phillips, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.229 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Medical implications from the crystal structure of a copper-containing amine oxidase complexed with the antidepressant drug tranylcypromine.

Wilmot, C.M., Saysell, C.G., Blessington, A., Conn, D.A., Kurtis, C.R., McPherson, M.J., Knowles, P.F., Phillips, S.E.

(2004) FEBS Lett 576: 301-305

• PubMed: 15498552 
• DOI: https://doi.org/10.1016/j.febslet.2004.09.031
• Primary Citation Related Structures: 
  1LVN


• PubMed Abstract: 
  

  The X-ray crystal structure of the copper-containing quinoprotein amine oxidase from E. coli has been determined in complex with the antidepressant drug tranylcypromine to 2.4 A resolution. The drug is a racemic mix of two enantiomers, but only one is seen bound to the enzyme. The other enantiomer is not acting as a substrate for the enzyme as no catalytic activity was detected when the enzyme was initially exposed to the drug. The inhibition of human copper amine oxidases could be a source of side-effects in its use as an antidepressant to inhibit the flavin-containing monoamine oxidases in the brain.

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Organizational Affiliation: 
• Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. [e-mail]

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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 163.26 kDa 
• Atom Count: 12,818 
• Modeled Residue Count: 1,438 
• Deposited Residue Count: 1,454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper amine oxidase	A, B	727	Escherichia coli	Mutation(s): 1  EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P46883 (Escherichia coli (strain K12)) Explore P46883  Go to UniProtKB:  P46883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CA	D [auth A], E [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYT	A, B	L-PEPTIDE LINKING	C18 H20 N2 O4		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.229 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.236	α = 90
b = 166.482	β = 90
c = 79.628	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAVATA	data reduction
CNS	refinement
CCP4	data scaling
ROTAVATA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-05 
Deposition Author(s): Wilmot, C.M., Phillips, S.E.

Revision History  

• Version 1.0: 2003-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 2.1: 2024-11-13
  Changes: Structure summary