Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 120.15 kDa 
• Atom Count: 8587 
• Modelled Residue Count: 993 
• Deposited Residue Count: 1040 
• Unique protein chains: 1

2XFQ

Rasagiline-inhibited human monoamine oxidase B in complex with 2-(2- benzofuranyl)-2-imidazoline

• PDB DOI: 10.2210/pdb2XFQ/pdb

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


• Deposited: 2010-05-26 Released: 2010-10-06 
• Deposition Author(s): Bonivento, D., Milczek, E.M., McDonald, G.R., Binda, C., Holt, A., Edmondson, D.E., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.159 

Literature

Potentiation of ligand binding through cooperative effects in monoamine oxidase B.

Bonivento, D., Milczek, E.M., McDonald, G.R., Binda, C., Holt, A., Edmondson, D.E., Mattevi, A.

(2010) J Biol Chem 285: 36849-36856

• PubMed: 20855894 
• DOI: 10.1074/jbc.M110.169482
• Primary Citation of Related Structures:  
  2XCG, 2XFN, 2XFO, 2XFP, 2XFQ, 2XFU


• PubMed Abstract: 
  

Crystallographic and biochemical studies have been employed to identify the binding site and mechanism for potentiation of imidazoline binding in human monoamine oxidase B (MAO B). 2-(2-Benzofuranyl)-2-imidazoline (2-BFI) inhibits recombinant human MAO B with a K(i) of 8.3 ± 0.6 μM, whereas tranylcypromine-inhibited MAO B binds 2-BFI with a K(d) of 9 ± 2 nM, representing an increase in binding energy Δ(ΔG) of -3.9 kcal/mol. Crystal structures show the imidazoline ligand bound in a site that is distinct from the substrate-binding cavity. Contributions to account for the increase in binding affinity upon tranylcypromine inhibition include a conformational change in the side chain of Gln(206) and a "closed conformation" of the side chain of Ile(199), forming a hydrophobic "sandwich" with the side chain of Ile(316) on each face of the benzofuran ring of 2-BFI. Data with the I199A mutant of human MAO B and failure to observe a similar binding potentiation with rat MAO B, where Ile(316) is replaced with a Val residue, support an allosteric mechanism where the increased binding affinity of 2-BFI results from a cooperative increase in H-bond strength through formation of a more hydrophobic milieu. These insights should prove valuable in the design of high affinity and specific reversible MAO B inhibitors.

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Organizational Affiliation: 

Department of Genetics and Microbiology, University of Pavia, I-27100 Pavia PV, Italy.

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 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
C15	F [auth A]	N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE C17 H38 N O3 S IZWSFJTYBVKZNK-UHFFFAOYSA-O
XCG	E [auth A], I [auth B]	2-(2-BENZOFURANYL)-2-IMIDAZOLINE C11 H8 N2 O VBFQIUOSXHUWCT-UHFFFAOYSA-N
RAS	D [auth A], H [auth B]	(1R)-N-(prop-2-en-1-yl)-2,3-dihydro-1H-inden-1-amine C12 H15 N RPAZWTZFMPXUKS-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.159 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.51	α = 90
b = 223.38	β = 90
c = 86.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-26 
• Released Date: 2010-10-06 
Deposition Author(s): Bonivento, D., Milczek, E.M., McDonald, G.R., Binda, C., Holt, A., Edmondson, D.E., Mattevi, A.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2012-02-29
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-12-20
  Changes: Database references
• Version 1.3: 2018-05-16
  Changes: Data collection
• Version 1.4: 2018-10-17
  Changes: Data collection, Database references, Source and taxonomy, Structure summary