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- PDB-7p4h: Crystal Structure of Monoamine Oxidase B in complex with inhibito... -

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Basic information

Entry
Database: PDB / ID: 7p4h
TitleCrystal Structure of Monoamine Oxidase B in complex with inhibitor (+)-2
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 / 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-5IH / Chem-C15 / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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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)120,4948
Polymers117,6752
Non-polymers2,8196
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-34 kcal/mol
Surface area36260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.831, 222.767, 86.288
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-867-

HOH

21B-770-

HOH

31B-798-

HOH

41B-871-

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-5IH / 3,4-dimethyl-7-[[(3~{S})-piperidin-3-yl]methoxy]chromen-2-one


Mass: 287.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.31 %
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: 0.9762 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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→47.45 Å / Num. obs: 70675 / % possible obs: 97.56 % / Redundancy: 4.4 % / CC1/2: 0.989 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.154 Å / Num. unique obs: 5244 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v5z

2v5z


Resolution: 2.1→47.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.614 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1850 2.6 %RANDOM
Rwork0.1676 ---
obs0.1688 70675 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.3 Å2 / Biso mean: 27.029 Å2 / Biso min: 13.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0 Å2
2---0.52 Å20 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 2.1→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 173 505 8592
Biso mean--30.53 32.19 -
Num. residues----993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138293
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177735
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6811280
X-RAY DIFFRACTIONr_angle_other_deg1.3121.59217938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8595991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55221.635416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.791151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0441558
X-RAY DIFFRACTIONr_chiral_restr0.0760.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021707
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 123 -
Rwork0.238 5244 -
all-5367 -
obs--98.59 %

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