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- PDB-2xfo: tranylcypromine-inhibited human monoamine oxidase B Ile199Ala mut... -

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Basic information

Entry
Database: PDB / ID: 2xfo
Titletranylcypromine-inhibited human monoamine oxidase B Ile199Ala mutant 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 / 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 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / 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 / : / Polyamine Oxidase; Chain A, domain 2 - #10 / Flavin amine oxidase / 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
3-PHENYLPROPANAL / Chem-FA8 / FLAVIN-ADENINE DINUCLEOTIDE / 2-(2-BENZOFURANYL)-2-IMIDAZOLINE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4May 16, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Jul 25, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.6Dec 20, 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 / 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 1.7Oct 9, 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

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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)119,8018
Polymers117,5912
Non-polymers2,2106
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-27 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.546, 221.863, 86.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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: 58795.652 Da / Num. of mol.: 2 / Mutation: 199A
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, 309 molecules

#2: Chemical ChemComp-FA8 / [[(2R,3S,4S)-5-[(4AS)-7,8-DIMETHYL-2,4-DIOXO-4A,5-DIHYDROBENZO[G]PTERIDIN-10-YL]-2,3,4-TRIHYDROXY-PENTOXY]-HYDROXY-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-3PL / 3-PHENYLPROPANAL


Mass: 134.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O
#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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 199 TO ALA ENGINEERED RESIDUE IN CHAIN B, ILE 199 TO ALA
Has protein modificationY
Nonpolymer detailsTRANYLCYPROMINE (TRA): CAK ATOM OF TRA IS COVALENTLY ATTACHED TO C4A ATOM OF FAD FLAVIN-ADENINE ...TRANYLCYPROMINE (TRA): CAK ATOM OF TRA IS COVALENTLY ATTACHED TO C4A ATOM OF FAD FLAVIN-ADENINE DINUCLEOTIDE (REDUCED) (FAD): C4A ATOM OF FAD IS COVALENTLY ATTACHED TO CAK ATOM OF TRA

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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: 2.72 Å3/Da / Density % sol: 54.78 % / 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 / Type: ESRF / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 69410 / % possible obs: 95.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.8 / % possible all: 97.6

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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 1OJB

1ojb
PDB Unreleased entry


Resolution: 2.1→65.27 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
Rfree0.243 -2.6 %RANDOM
Rwork0.189 ---
obs0.19 67613 94.96 %-
Refinement stepCycle: LAST / Resolution: 2.1→65.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 154 303 8365

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