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- PDB-6fwc: Crystal structure of human monoamine oxidase B (MAO B) in complex... -

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Basic information

Entry
Database: PDB / ID: 6fwc
TitleCrystal structure of human monoamine oxidase B (MAO B) in complex with fluorophenyl-chromone-carboxamide
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / Parkinson's disease / drug design / chromone / inhibitor
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
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / : / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-C15 / Chem-E98 / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsReis, J. / Manzella, N. / Cagide, F. / Mialet-Perez, J. / Uriarte, E. / Parini, A. / Borges, F. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO2014-0672 Italy
CitationJournal: J. Med. Chem. / Year: 2018
Title: Tight-Binding Inhibition of Human Monoamine Oxidase B by Chromone Analogs: A Kinetic, Crystallographic, and Biological Analysis.
Authors: Reis, J. / Manzella, N. / Cagide, F. / Mialet-Perez, J. / Uriarte, E. / Parini, A. / Borges, F. / Binda, C.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Apr 22, 2020Group: Author supporting evidence / Database references / Category: pdbx_audit_support / pdbx_related_exp_data_set / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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)120,67010
Polymers117,6752
Non-polymers2,9958
Water18,1051005
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-35 kcal/mol
Surface area36240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.728, 222.051, 86.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-845-

HOH

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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, 1013 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-E98 / ~{N}-(3-fluorophenyl)-4-oxidanylidene-chromene-3-carboxamide


Mass: 283.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H10FNO3
#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.: 1005 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 12% PEG4000, 100 mM ADA pH 6.5, 70 mM lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 1.02 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.7→47.3 Å / Num. obs: 137691 / % possible obs: 99.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.083 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v5z

2v5z


Resolution: 1.7→47.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.972 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18946 3408 2.5 %RANDOM
Rwork0.16157 ---
obs0.16227 134282 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0 Å2
2---0.57 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 187 1005 9106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198331
X-RAY DIFFRACTIONr_bond_other_d0.0020.027751
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.99211330
X-RAY DIFFRACTIONr_angle_other_deg1.513.00117978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07451001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5623.538359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.807151417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4051558
X-RAY DIFFRACTIONr_chiral_restr0.0840.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021654
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9521.4713980
X-RAY DIFFRACTIONr_mcbond_other0.9511.473979
X-RAY DIFFRACTIONr_mcangle_it1.5622.1994974
X-RAY DIFFRACTIONr_mcangle_other1.5622.24975
X-RAY DIFFRACTIONr_scbond_it1.5741.6964350
X-RAY DIFFRACTIONr_scbond_other1.5741.6964350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5232.4646352
X-RAY DIFFRACTIONr_long_range_B_refined4.24618.2839871
X-RAY DIFFRACTIONr_long_range_B_other3.96717.6859603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 254 -
Rwork0.247 9802 -
obs--98.9 %

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