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- PDB-7zw3: Crystal Structure of human MAO B in complex with (Z)-N-benzyl-1-(... -

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Basic information

Entry
Database: PDB / ID: 7zw3
TitleCrystal Structure of human MAO B in complex with (Z)-N-benzyl-1-(8-hydroxyquinolin-2-yl)methanimine oxide (inhibitor 19)
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / Monoamine Oxidase / Alzheimer's disease / enzyme / drug / mitochondrial membrane
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
: / Flavin amine oxidase / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-AI0 / Chem-C15 / 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. / Gottinger, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Acta Pharm Sin B / Year: 2023
Title: 8-Hydroxyquinolylnitrones as multifunctional ligands for the therapy of neurodegenerative diseases.
Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. ...Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. / Stojan, J. / Salat, K. / Serrano, J. / Fernandez, A.P. / Sanchez-Garcia, A. / Martinez-Murillo, R. / Binda, C. / Lopez-Munoz, F. / Gobec, S. / Marco-Contelles, J.
History
DepositionMay 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Amine oxidase [flavin-containing] B
BBB: Amine oxidase [flavin-containing] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4768
Polymers117,6752
Non-polymers2,8016
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-33 kcal/mol
Surface area36110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.644, 222.399, 86.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) / Strain (production host): KM71 / 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-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO3S
#4: Chemical ChemComp-AI0 / 1-(8-oxidanylquinolin-2-yl)-N-(phenylmethyl)methanimine oxide / (Z)-N-benzyl-1-(8-hydroxyquinolin-2-yl)methanimine oxide


Mass: 278.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12 % (w/v) PEG 4000, 100 mM ADA buffer pH 6.5, 70 mM Lithium Sulfate, 4.5 mM Zwittergent 3-12

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2→47.34 Å / Num. obs: 84901 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.117 / Rrim(I) all: 0.207 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.04 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4484 / CC1/2: 0.617 / Rpim(I) all: 0.628 / Rrim(I) all: 0.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V5Z

2v5z


Resolution: 2→47.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.725 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2042 2205 2.598 %
Rwork0.1661 82667 -
all0.167 --
obs-84872 99.156 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.933 Å2
Baniso -1Baniso -2Baniso -3
1-1.635 Å20 Å2-0 Å2
2---1.223 Å20 Å2
3----0.412 Å2
Refinement stepCycle: LAST / Resolution: 2→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 174 689 8789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177902
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.67211370
X-RAY DIFFRACTIONr_angle_other_deg1.7641.58418235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72751011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01821.655417
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.969151428
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg21.092152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6241558
X-RAY DIFFRACTIONr_chiral_restr0.0760.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021862
X-RAY DIFFRACTIONr_nbd_refined0.2010.21677
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.27486
X-RAY DIFFRACTIONr_nbtor_refined0.1690.24033
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2567
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1780.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3730.29
X-RAY DIFFRACTIONr_nbd_other0.2780.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6280.233
X-RAY DIFFRACTIONr_mcbond_it1.6172.0683996
X-RAY DIFFRACTIONr_mcbond_other1.6132.0673995
X-RAY DIFFRACTIONr_mcangle_it2.3183.0914996
X-RAY DIFFRACTIONr_mcangle_other2.3193.0924997
X-RAY DIFFRACTIONr_scbond_it2.6882.4354358
X-RAY DIFFRACTIONr_scbond_other2.6882.4364359
X-RAY DIFFRACTIONr_scangle_it4.1583.536365
X-RAY DIFFRACTIONr_scangle_other4.1573.5316366
X-RAY DIFFRACTIONr_lrange_it5.5224.919666
X-RAY DIFFRACTIONr_lrange_other5.44624.6859536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2621850.2366118X-RAY DIFFRACTION99.7468
2.052-2.1080.2521370.2235910X-RAY DIFFRACTION99.6047
2.108-2.1690.2181510.2045733X-RAY DIFFRACTION99.5938
2.169-2.2360.221540.1855584X-RAY DIFFRACTION99.3249
2.236-2.3090.2131440.1775483X-RAY DIFFRACTION99.4697
2.309-2.390.1711360.1615256X-RAY DIFFRACTION99.465
2.39-2.480.1681470.165019X-RAY DIFFRACTION99.3462
2.48-2.5820.2431210.1684906X-RAY DIFFRACTION99.3871
2.582-2.6960.2051380.1684676X-RAY DIFFRACTION99.3602
2.696-2.8280.2151350.1674457X-RAY DIFFRACTION99.3294
2.828-2.9810.1891080.1614311X-RAY DIFFRACTION99.7742
2.981-3.1620.21860.1584084X-RAY DIFFRACTION99.8085
3.162-3.380.191020.1473772X-RAY DIFFRACTION98.2003
3.38-3.650.192910.1523515X-RAY DIFFRACTION98.3633
3.65-3.9980.182860.1463265X-RAY DIFFRACTION98.7331
3.998-4.4690.192810.1392980X-RAY DIFFRACTION98.7738
4.469-5.1590.195690.1372650X-RAY DIFFRACTION98.8368
5.159-6.3160.205650.172218X-RAY DIFFRACTION98.2358
6.316-8.9180.179440.1541744X-RAY DIFFRACTION97.2796
8.918-47.340.285250.209986X-RAY DIFFRACTION92.6673

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