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- PDB-2vz2: Human MAO B in complex with mofegiline -

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Basic information

Entry
Database: PDB / ID: 2vz2
TitleHuman MAO B in complex with mofegiline
ComponentsAMINE OXIDASE [FLAVIN-CONTAINING] B
KeywordsOXIDOREDUCTASE / INHIBITOR BINDING / FLAVOPROTEIN / MITOCHONDRION / TRANSMEMBRANE / HUMAN MONOAMINE OXIDASE / MITOCHONDRION OUTER MEMBRANE / FAD / FLAVIN / MEMBRANE / MOFEGILINE / ACETYLATION
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 / FLAVIN-ADENINE DINUCLEOTIDE / Chem-MFG / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBonivento, D. / Mattevi, A.
CitationJournal: J. Med. Chem. / Year: 2008
Title: Structural and mechanistic studies of mofegiline inhibition of recombinant human monoamine oxidase B.
Authors: Milczek, E.M. / Bonivento, D. / Binda, C. / Mattevi, A. / McDonald, I.A. / Edmondson, D.E.
History
DepositionJul 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _struct.title
Revision 1.4Dec 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 / pdbx_struct_special_symmetry / struct_conn / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)120,2748
Polymers117,6752
Non-polymers2,5996
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-7.5 kcal/mol
Surface area45190 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.026, 223.730, 86.629
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-2142-

HOH

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

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A3 - 600
2115B3 - 600

NCS oper: (Code: given
Matrix: (-0.53369, -0.48972, -0.68946), (-0.49333, -0.48189, 0.72416), (-0.68688, 0.7266, 0.01559)
Vector: 139.53241, 209.46535, -55.00652)

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Components

#1: Protein AMINE OXIDASE [FLAVIN-CONTAINING] B / HUMAN MONOAMINE OXIDASE B / MAO-B / MONOAMINE OXIDASE TYPE B


Mass: 58837.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN FAD AND MOFEGILINE INHIBITOR / 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-MFG / (1Z)-4-(4-FLUOROPHENYL)-2-METHYLIDENEBUTAN-1-IMINE


Mass: 177.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12FN
#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.: 433 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMOFEGILINE (MFG): COVALENT BOND WITH FAD N5 ATOM, FLUORINE ELIMINATION UPON BINDING

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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: 53.73 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 55954 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJA

1oja


Resolution: 2.3→29.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.241 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1449 2.6 %RANDOM
Rwork0.187 ---
obs0.188 54490 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---0.85 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 176 433 8523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228302
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.99111282
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60923.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28151413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3971558
X-RAY DIFFRACTIONr_chiral_restr0.0710.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.23991
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25633
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.55112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65328016
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.01133747
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6244.53265
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 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1975medium positional0.130.5
2026loose positional0.395
1975medium thermal0.32
2026loose thermal0.7510
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 106
Rwork0.193 4072

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