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- PDB-7p4f: Crystal Structure of Monoamine Oxidase B in complex with inhibitor 1 -

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Basic information

Entry
Database: PDB / ID: 7p4f
TitleCrystal Structure of Monoamine Oxidase B in complex with inhibitor 1
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / monoamine oxidase / drug target / neurodegeneration / mitochondrial membrane
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / response to corticosterone / substantia nigra development / response to toxic substance / flavin adenine dinucleotide binding / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / response to xenobiotic stimulus / neuronal cell body / dendrite / mitochondrion / identical protein binding
Similarity search - Function
: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-5IK / Chem-C15 / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIacovino, L.G. / Binda, C. / Pisani, L.
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Dual Reversible Coumarin Inhibitors Mutually Bound to Monoamine Oxidase B and Acetylcholinesterase Crystal Structures.
Authors: Ekstrom, F. / Gottinger, A. / Forsgren, N. / Catto, M. / Iacovino, L.G. / Pisani, L. / Binda, C.
History
DepositionJul 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amine oxidase [flavin-containing] B
B: Amine oxidase [flavin-containing] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7518
Polymers117,6752
Non-polymers3,0756
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-36 kcal/mol
Surface area35990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.243, 222.428, 86.206
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-881-

HOH

21B-839-

HOH

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Components

#1: Protein Amine oxidase [flavin-containing] B / Monoamine oxidase type B / MAO-B


Mass: 58837.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Production host: Komagataella pastoris (fungus) / References: UniProt: P27338, monoamine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-5IK / 4-(hydroxymethyl)-7-[[4-[[methyl-(phenylmethyl)amino]methyl]phenyl]methoxy]chromen-2-one


Mass: 415.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25NO4
#4: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG 4000, lithium sulfate, ADA buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→47.31 Å / Num. obs: 54746 / % possible obs: 99.6 % / Redundancy: 5.3 % / CC1/2: 0.99 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 4014 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v5z

2v5z


Resolution: 2.3→47.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.734 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 1455 2.6 %RANDOM
Rwork0.1613 ---
obs0.1627 54746 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.17 Å2 / Biso mean: 28.935 Å2 / Biso min: 10.84 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å2-0 Å2
2---2.06 Å20 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 2.3→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 193 383 8490
Biso mean--27.86 29.87 -
Num. residues----993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0148317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177513
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.69911306
X-RAY DIFFRACTIONr_angle_other_deg1.4721.65317606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42721.635416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.653151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0631558
X-RAY DIFFRACTIONr_chiral_restr0.0680.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 99 -
Rwork0.205 4014 -
all-4113 -
obs--99.81 %

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