3PO7

Human monoamine oxidase B in complex with zonisamide

• PDB DOI: https://doi.org/10.2210/pdb3PO7/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2010-11-22 Released: 2011-01-12 
• Deposition Author(s): Binda, C., Aldeco, M., Mattevi, A., Edmondson, D.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Interactions of monoamine oxidases with the antiepileptic drug zonisamide: specificity of inhibition and structure of the human monoamine oxidase B complex

Binda, C., Aldeco, M., Mattevi, A., Edmondson, D.E.

(2011) J Med Chem 54: 909-912

• PubMed: 21175212 
• DOI: https://doi.org/10.1021/jm101359c
• Primary Citation of Related Structures:  
  3PO7


• PubMed Abstract: 
  

  The binding of zonisamide to purified, recombinant monoamine oxidases (MAOs) has been investigated. It is a competitive inhibitor of human MAO B (K(i) = 3.1 ± 0.3 μM), of rat MAO B (K(i) = 2.9 ± 0.5 μM), and of zebrafish MAO (K(i) = 30.8 ± 5.3 μM). No inhibition is observed with purified human or rat MAO A. The 1.8 Å structure of the MAO B complex demonstrates that it binds within the substrate cavity.

---

Organizational Affiliation: 

Department Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia 27100, Italy.

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: 119.67 kDa 
• Atom Count: 8,794 
• Modelled Residue Count: 993 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amine oxidase [flavin-containing] B	A, B	520	Homo sapiens	Mutation(s): 0  Gene Names: MAOB EC: 1.4.3.4 (PDB Primary Data), 1.4.3.21 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P27338 (Homo sapiens) Explore P27338  Go to UniProtKB:  P27338
PHAROS:  P27338 GTEx:  ENSG00000069535

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
ZON	D [auth A], F [auth B]	1-(1,2-benzoxazol-3-yl)methanesulfonamide C8 H8 N2 O3 S UBQNRHZMVUUOMG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZON	BindingDB:  3PO7	Ki: min: 2900, max: 3100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.4	α = 90
b = 222.6	β = 90
c = 86.19	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Binda, C., Aldeco, M., Mattevi, A., Edmondson, D.E.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-03-05
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary