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- PDB-5mrl: Crystal structure of human monoamine oxidase B (MAO B) in complex... -

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Basic information

Entry
Database: PDB / ID: 5mrl
TitleCrystal structure of human monoamine oxidase B (MAO B) in complex with N(Furan2ylmethyl)Nmethylprop2yn1amine (F2MPA)
ComponentsAmine oxidase [flavin-containing] B
KeywordsOXIDOREDUCTASE / monoamine oxidase / neurodegeneration / inhibitor / enzyme
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-F2M / FLAVIN-ADENINE DINUCLEOTIDE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsBinda, C. / De Deurwaerdere, P. / Corne, R. / Leone, C. / Valeri, A. / Valoti, M. / Ramsay, R.R. / Fall, Y. / Marco-Contelles, J.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO2014-0672 Italy
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Comparative Analysis of the Neurochemical Profile and MAO Inhibition Properties of N-(Furan-2-ylmethyl)-N-methylprop-2-yn-1-amine.
Authors: De Deurwaerdere, P. / Binda, C. / Corne, R. / Leone, C. / Valeri, A. / Valoti, M. / Ramsay, R.R. / Fall, Y. / Marco-Contelles, J.
History
DepositionDec 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Nov 13, 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)119,5496
Polymers117,6752
Non-polymers1,8744
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-34 kcal/mol
Surface area36420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.848, 223.239, 86.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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: Komagataella 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-F2M / (~{E})-~{N}-(furan-2-ylmethyl)-~{N}-methyl-prop-1-en-1-amine / F2MPA


Mass: 151.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG4000, ADA, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→113 Å / Num. obs: 48068 / % possible obs: 98.4 % / Redundancy: 7.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 4 / CC1/2: 0.781 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v5z

2v5z


Resolution: 2.42→113 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.871 / SU B: 7.003 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23425 1251 2.6 %RANDOM
Rwork0.16776 ---
obs0.16946 46779 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.341 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å2-0 Å2
2---1.1 Å20 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 2.42→113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 128 268 8310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198250
X-RAY DIFFRACTIONr_bond_other_d0.0060.027853
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.98411207
X-RAY DIFFRACTIONr_angle_other_deg1.566318093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29623.52358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.423151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5421558
X-RAY DIFFRACTIONr_chiral_restr0.0980.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219115
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021817
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_it1.7692.3093970
X-RAY DIFFRACTIONr_mcbond_other1.7612.3083969
X-RAY DIFFRACTIONr_mcangle_it2.7943.4544959
X-RAY DIFFRACTIONr_mcangle_other2.7953.4564960
X-RAY DIFFRACTIONr_scbond_it2.6982.6724280
X-RAY DIFFRACTIONr_scbond_other2.6972.6734281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2963.8646249
X-RAY DIFFRACTIONr_long_range_B_refined5.78618.489363
X-RAY DIFFRACTIONr_long_range_B_other5.76518.4719312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.421→2.484 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 104 -
Rwork0.228 3241 -
obs--93.07 %

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