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- PDB-3po7: Human monoamine oxidase B in complex with zonisamide -

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Basic information

Entry
Database: PDB / ID: 3po7
TitleHuman monoamine oxidase B in complex with zonisamide
ComponentsAmine oxidase [flavin-containing] B
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / flavin-binding amine oxidase / neurotransmitter metabolism / FAD / mitochondrial outer membrane / antiparkinson drug / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
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
FLAVIN-ADENINE DINUCLEOTIDE / 1-(1,2-benzoxazol-3-yl)methanesulfonamide / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBinda, C. / Aldeco, M. / Mattevi, A. / Edmondson, D.E.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Interactions of monoamine oxidases with the antiepileptic drug zonisamide: specificity of inhibition and structure of the human monoamine oxidase B complex
Authors: Binda, C. / Aldeco, M. / Mattevi, A. / Edmondson, D.E.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)119,6716
Polymers117,6752
Non-polymers1,9964
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-16 kcal/mol
Surface area37230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.400, 222.600, 86.190
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-583-

HOH

21B-587-

HOH

31B-899-

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: Pichia 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-ZON / 1-(1,2-benzoxazol-3-yl)methanesulfonamide / Zonisamide


Mass: 212.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8N2O3S / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H2O

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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: 54.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG 4000, 100mM ADA pH 6.5, 70mM Lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2010
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→47.3 Å / Num. all: 115434 / Num. obs: 115434 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2v5z

2v5z


Resolution: 1.8→47.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.183 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21198 2924 2.5 %RANDOM
Rwork0.18179 ---
all0.185 115434 --
obs0.18256 112363 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.256 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 134 749 8794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228249
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.98611215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14823.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.036151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2551558
X-RAY DIFFRACTIONr_chiral_restr0.0770.21221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216198
X-RAY DIFFRACTIONr_mcbond_it0.4991.54942
X-RAY DIFFRACTIONr_mcangle_it0.98628008
X-RAY DIFFRACTIONr_scbond_it1.67933307
X-RAY DIFFRACTIONr_scangle_it2.8374.53207
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 183 -
Rwork0.252 8205 -
obs--98.12 %

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