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- PDB-2v61: Structure of human MAO B in complex with the selective inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 2v61
TitleStructure of human MAO B in complex with the selective inhibitor 7-(3- chlorobenzyloxy)-4-(methylamino)methyl-coumarin
ComponentsAMINE OXIDASE (FLAVIN-CONTAINING) B
KeywordsOXIDOREDUCTASE / FAD / MEMBRANE / SAFINAMIDE / FLAVOPROTEIN / HUMAN MAO B STRUCTURE / REVERSIBLE INHIBITOR BINDING / MITOCHONDRION / TRANSMEMBRANE / NEUROPROTECTION / PARKINSON'S DISEASE
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / 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 / dopamine catabolic process ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / 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 / dopamine catabolic process / aliphatic amine oxidase activity / primary methylamine oxidase activity / 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 / 3-Layer(bba) Sandwich ...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-C18 / 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
AuthorsBinda, C. / Wang, J. / Pisani, L. / Caccia, C. / Carotti, A. / Salvati, P. / Edmondson, D.E. / Mattevi, A.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Structures of Human Monoamine Oxidase B Complexes with Selective Noncovalent Inhibitors: Safinamide and Coumarin Analogs.
Authors: Binda, C. / Wang, J. / Pisani, L. / Caccia, C. / Carotti, A. / Salvati, P. / Edmondson, D.E. / Mattevi, A.
History
DepositionJul 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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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)119,9066
Polymers117,6752
Non-polymers2,2314
Water16,592921
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-10.8 kcal/mol
Surface area44020 Å2
MethodPQS
Unit cell
Length a, b, c (Å)131.998, 222.539, 86.202
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
11A-1013-

HOH

21B-1029-

HOH

31B-1097-

HOH

41B-1175-

HOH

51B-1312-

HOH

61B-1364-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 99
2114B3 - 99
1214A110 - 496
2214B110 - 496
1314A600
2314B600
1414A601
2414B601

NCS oper: (Code: given
Matrix: (-0.53016, -0.49489, -0.68849), (-0.49323, -0.48046, 0.72517), (0.68967, 0.72404, 0.01063)
Vector: 139.5977, 207.98894, -53.79338)

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Components

#1: Protein AMINE OXIDASE (FLAVIN-CONTAINING) B / MONOAMINE OXIDASE TYPE B / MAO-B / MONOAMINE OXIDASE


Mass: 58837.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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-C18 / 7-[(3-CHLOROBENZYL)OXY]-4-[(METHYLAMINO)METHYL]-2H-CHROMEN-2-ONE


Mass: 329.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16ClNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 50.74 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 138335 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJA

1oja


Resolution: 1.7→113.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.49 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM C4N OF THE INHIBITOR IS NOT DEFINED IN THE ELECTRON DENSITY AND HAS BEEN ASSIGNED OCCUPANCY 0.00
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3505 2.5 %RANDOM
Rwork0.172 ---
obs0.173 134828 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→113.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 152 921 8984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.98911247
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63123.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.945151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4261558
X-RAY DIFFRACTIONr_chiral_restr0.0860.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026220
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.24299
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2777
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3420.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.55074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15328008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02633748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1344.53239
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3933 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.120.5
medium thermal0.72
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 268
Rwork0.212 9846

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