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- PDB-6rkp: Crystal structure of human monoamine oxidase B in complex with st... -

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Basic information

Entry
Database: PDB / ID: 6rkp
TitleCrystal structure of human monoamine oxidase B in complex with styrylpiperidine analogue 84
ComponentsAmine oxidase [flavin-containing] B
KeywordsFLAVOPROTEIN / monoamine oxidase / drug target / neurodegeneration / flavin / isomer / 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
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-K72 / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsIacovino, L.G. / Knez, D. / Colettis, N. / Sova, M. / Pislar, A. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. ...Iacovino, L.G. / Knez, D. / Colettis, N. / Sova, M. / Pislar, A. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. / Trontelj, J. / Kos, J. / Marder, N.M. / Gobec, S. / Binda, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO2014-0672 Italy
CitationJournal: J.Med.Chem. / Year: 2020
Title: Stereoselective Activity of 1-Propargyl-4-styrylpiperidine-like Analogues That Can Discriminate between Monoamine Oxidase Isoforms A and B.
Authors: Knez, D. / Colettis, N. / Iacovino, L.G. / Sova, M. / Pislar, A. / Konc, J. / Lesnik, S. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. / Trontelj, J. / Kos, J. / ...Authors: Knez, D. / Colettis, N. / Iacovino, L.G. / Sova, M. / Pislar, A. / Konc, J. / Lesnik, S. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. / Trontelj, J. / Kos, J. / Binda, C. / Marder, M. / Gobec, S.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)120,69510
Polymers117,6752
Non-polymers3,0198
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-37 kcal/mol
Surface area36560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.908, 223.657, 86.721
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-1029-

HOH

21B-771-

HOH

31B-877-

HOH

41B-883-

HOH

51B-1001-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 777 molecules

#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-K72 / 1-[(~{E})-prop-1-enyl]-4-[(~{E})-2-[4-(trifluoromethyl)phenyl]ethenyl]piperidine


Mass: 295.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20F3N
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, lithium sulphate, ADA buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→47.71 Å / Num. obs: 141411 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.666 / Num. unique obs: 6932 / CC1/2: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v5z

2v5z


Resolution: 1.7→47.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.264 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20558 3545 2.5 %RANDOM
Rwork0.18137 ---
obs0.18199 137863 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.534 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-0 Å2
2---0.63 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 186 769 8869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0148306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177517
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.69411285
X-RAY DIFFRACTIONr_angle_other_deg1.4781.65317619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14721.635416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.916151410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2341558
X-RAY DIFFRACTIONr_chiral_restr0.0650.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
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_it1.3282.1853970
X-RAY DIFFRACTIONr_mcbond_other1.3282.1843969
X-RAY DIFFRACTIONr_mcangle_it1.9933.2674959
X-RAY DIFFRACTIONr_mcangle_other1.9933.2694960
X-RAY DIFFRACTIONr_scbond_it2.1392.5084335
X-RAY DIFFRACTIONr_scbond_other2.1392.5084335
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4263.6446327
X-RAY DIFFRACTIONr_long_range_B_refined4.6825.8299320
X-RAY DIFFRACTIONr_long_range_B_other4.5925.4669156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 245 -
Rwork0.551 10107 -
obs--99.95 %

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