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- PDB-7b0v: Crystal Structure of human monoamine oxidase B in complex with (E... -

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Basic information

Entry
Database: PDB / ID: 7b0v
TitleCrystal Structure of human monoamine oxidase B in complex with (E)-3-phenyl-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / monoamine oxidase / drug target / neurodegeneration / flavin / chalcone / mitochondrial membrane
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / dopamine catabolic process / mitochondrial envelope / hydrogen peroxide biosynthetic process / substantia nigra development / flavin adenine dinucleotide binding / mitochondrial outer membrane / electron transfer activity / mitochondrion
Similarity search - Function
: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-C15 / FLAVIN-ADENINE DINUCLEOTIDE / Chem-SKB / 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.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Promising Non-cytotoxic Monosubstituted Chalcones to Target Monoamine Oxidase-B.
Authors: Iacovino, L.G. / Pinzi, L. / Facchetti, G. / Bortolini, B. / Christodoulou, M.S. / Binda, C. / Rastelli, G. / Rimoldi, I. / Passarella, D. / Di Paolo, M.L. / Dalla Via, L.
History
DepositionNov 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)120,65610
Polymers117,6752
Non-polymers2,9818
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-38 kcal/mol
Surface area36060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.654, 221.798, 85.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 460 molecules

#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-SKB / (E)-3-phenyl-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one / (~{E})-3-phenyl-1-[3-(trifluoromethyl)phenyl]prop-2-en-1-one


Mass: 276.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11F3O / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 4000, lithium sulphate, ADA buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→47.12 Å / Num. obs: 52922 / % possible obs: 99.91 % / Redundancy: 7.3 % / CC1/2: 0.99 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 3823 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v5z

2v5z


Resolution: 2.3→47.12 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.823 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 2786 5 %RANDOM
Rwork0.1679 ---
obs0.1689 52922 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.74 Å2 / Biso mean: 17.357 Å2 / Biso min: 3.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---1.64 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.3→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 184 452 8547
Biso mean--22.18 19.9 -
Num. residues----993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0138321
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177742
X-RAY DIFFRACTIONr_angle_refined_deg1.621.65811318
X-RAY DIFFRACTIONr_angle_other_deg1.3041.57617960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22351001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46921.635416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.921558
X-RAY DIFFRACTIONr_chiral_restr0.0740.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021744
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 233 -
Rwork0.19 3823 -
all-4056 -
obs--99.98 %

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