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- PDB-2xfq: Rasagiline-inhibited human monoamine oxidase B in complex with 2-... -

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Basic information

Entry
Database: PDB / ID: 2xfq
TitleRasagiline-inhibited human monoamine oxidase B in complex with 2-(2- benzofuranyl)-2-imidazoline
ComponentsAmine oxidase [flavin-containing] B
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN
Function / homology
Function and homology information


Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion / : / dopamine catabolic process / primary-amine oxidase / mitochondrial envelope / hydrogen peroxide biosynthetic process / response to corticosterone / substantia nigra development / response to toxic substance / flavin adenine dinucleotide binding / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / response to xenobiotic stimulus / dendrite / neuronal cell body / mitochondrion / identical protein binding
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 / 3-Layer(bba) Sandwich ...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-RAS / 2-(2-BENZOFURANYL)-2-IMIDAZOLINE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBonivento, D. / Milczek, E.M. / McDonald, G.R. / Binda, C. / Holt, A. / Edmondson, D.E. / Mattevi, A.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Potentiation of ligand binding through cooperative effects in monoamine oxidase B.
Authors: Bonivento, D. / Milczek, E.M. / McDonald, G.R. / Binda, C. / Holt, A. / Edmondson, D.E. / Mattevi, A.
History
DepositionMay 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Non-polymer description / Version format compliance
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
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
Revision 1.3May 16, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Oct 17, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_name_com / entity_src_gen / entity_src_nat / struct / struct_ref
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type ..._diffrn_source.pdbx_wavelength_list / _diffrn_source.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct.title / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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

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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)120,2989
Polymers117,6752
Non-polymers2,6237
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-28 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.510, 223.380, 86.550
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-2003-

HOH

21B-2154-

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, 479 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-RAS / (1R)-N-(prop-2-en-1-yl)-2,3-dihydro-1H-inden-1-amine / RASAGILINE, BOUND FORM / Rasagiline


Mass: 173.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N / Comment: inhibitor*YM
#4: Chemical ChemComp-XCG / 2-(2-BENZOFURANYL)-2-IMIDAZOLINE


Mass: 184.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8N2O
#5: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H38NO3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFLAVIN-ADENINE DINUCLEOTIDE (FAD): N5 ATOM OF FAD IS COVALENTLY ATTACHED TO C13 ATOM OF RAS N- ...FLAVIN-ADENINE DINUCLEOTIDE (FAD): N5 ATOM OF FAD IS COVALENTLY ATTACHED TO C13 ATOM OF RAS N-PROPARGYL-1(R)-AMINOINDAN (RASAGILINE) (RAS): C13 ATOM OF RAS IS COVALENTLY ATTACHED TO N5 ATOM OF FAD

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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: 54.46 % / 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: ID14-4 / Wavelength: 1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 64575 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 4 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2Q

1s2q


Resolution: 2.2→40.4 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rwork0.159 ---
obs-62931 98.9 %-
Rfree---RANDOM
Refinement stepCycle: LAST / Resolution: 2.2→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 182 472 8568

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