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- PDB-2xcg: Tranylcypromine-inhibited human monoamine oxidase B in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2xcg
TitleTranylcypromine-inhibited human monoamine oxidase B in complex with 2- (2-benzofuranyl)-2-imidazoline
ComponentsAmine oxidase [flavin-containing] B
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / MAOB / MITOCHONDRION / TRANSMEMBRANE
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-C15 / Chem-FA8 / 2-(2-BENZOFURANYL)-2-IMIDAZOLINE / Amine oxidase [flavin-containing] B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionApr 23, 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 1.5Oct 17, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_struct_special_symmetry / 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 1.6Dec 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 6, 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
A: Amine oxidase [flavin-containing] B
B: Amine oxidase [flavin-containing] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,56010
Polymers117,6752
Non-polymers2,8858
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-37.9 kcal/mol
Surface area37180 Å2
MethodPISA
2
A: Amine oxidase [flavin-containing] B
B: Amine oxidase [flavin-containing] B
hetero molecules

A: Amine oxidase [flavin-containing] B
B: Amine oxidase [flavin-containing] B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,12120
Polymers235,3514
Non-polymers5,77016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x+1/2,-y+3/2,z1
Buried area21880 Å2
ΔGint-85.9 kcal/mol
Surface area71220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.893, 223.706, 86.716
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-2008-

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, 762 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.: 2 / 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-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H38NO3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTRANYLCYPROMINE COVALENTLY ATTACHED TO FAD. FLAVIN-ADENINE DINUCLEOTIDE LEAVING FA8 COMPLEXED TO 3PL.

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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: 2.56 Å3/Da / Density % sol: 51.63 % / Description: NONE
Crystal growpH: 6.5 / Details: PEG 4000 12%, LISO4 70MM, ADA 0.1M 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: 1.9→50 Å / Num. obs: 100933 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rmerge(I) obs: 0.1

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Processing

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

1ojb
PDB Unreleased entry


Resolution: 1.9→46.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.149 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18941 2553 2.5 %RANDOM
Rwork0.15514 ---
obs0.15601 98378 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 198 754 8866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0228378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.99711384
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94151011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17423.518361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.288151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3631559
X-RAY DIFFRACTIONr_chiral_restr0.1160.21234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216273
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.831.54972
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47728070
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.56333406
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1954.53304
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 183 -
Rwork0.188 7177 -
obs--100 %

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