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- PDB-2v60: Structure of human MAO B in complex with the selective inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 2v60
TitleStructure of human MAO B in complex with the selective inhibitor 7-(3- chlorobenzyloxy)-4-carboxaldehyde-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 / 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 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / 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 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / 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-C17 / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 12, 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
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)119,8766
Polymers117,6752
Non-polymers2,2014
Water13,619756
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-13.2 kcal/mol
Surface area44460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)130.694, 224.413, 86.811
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-1038-

HOH

21B-1079-

HOH

31B-1255-

HOH

41B-1257-

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: (-0.52574, -0.49539, -0.69151), (-0.49594, -0.48197, 0.72232), (-0.69112, 0.7227, 0.00771)
Vector: 140.00504, 210.02158, -54.68348)

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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-C17 / 7-[(3-CHLOROBENZYL)OXY]-2-OXO-2H-CHROMENE-4-CARBALDEHYDE


Mass: 314.720 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H11ClO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 51.92 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 85456 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.13

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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: 2→113.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.339 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2206 2.6 %RANDOM
Rwork0.172 ---
obs0.174 83205 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2→113.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 150 756 8817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.98911245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07823.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.295151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3021558
X-RAY DIFFRACTIONr_chiral_restr0.1040.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026222
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23908
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25546
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4020.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0071.55144
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49428008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57733776
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8774.53237
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: 3932 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.20.5
medium thermal0.972
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 158
Rwork0.235 6056

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