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- PDB-2bxs: Human Monoamine Oxidase A in complex with Clorgyline, Crystal Form B -

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Basic information

Entry
Database: PDB / ID: 2bxs
TitleHuman Monoamine Oxidase A in complex with Clorgyline, Crystal Form B
ComponentsAMINE OXIDASE [FLAVIN-CONTAINING] A
KeywordsOXIDOREDUCTASE / NEUROTRANSMITTER / MEMBRANE-PROTEIN / FLAVIN
Function / homology
Function and homology information


Defective MAOA causes BRUNS / biogenic amine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Dopamine clearance from the synaptic cleft / Metabolism of serotonin / Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / positive regulation of signal transduction ...Defective MAOA causes BRUNS / biogenic amine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Dopamine clearance from the synaptic cleft / Metabolism of serotonin / Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / positive regulation of signal transduction / Norepinephrine Neurotransmitter Release Cycle / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / dopamine catabolic process / flavin adenine dinucleotide binding / Interleukin-4 and Interleukin-13 signaling / mitochondrial outer membrane / mitochondrion / cytosol
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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-MLG / Amine oxidase [flavin-containing] A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsDe Colibus, L. / Binda, C. / Edmondson, D.E. / Mattevi, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Three-Dimensional Structure of Human Monoamine Oxidase a (Mao A): Relation to the Structures of Rat Mao a and Human Mao B
Authors: De Colibus, L. / Li, M. / Binda, C. / Lustig, A. / Edmondson, D.E. / Mattevi, A.
History
DepositionJul 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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] A
B: AMINE OXIDASE [FLAVIN-CONTAINING] A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6346
Polymers119,5192
Non-polymers2,1154
Water00
1
A: AMINE OXIDASE [FLAVIN-CONTAINING] A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8173
Polymers59,7601
Non-polymers1,0582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: AMINE OXIDASE [FLAVIN-CONTAINING] A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8173
Polymers59,7601
Non-polymers1,0582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.374, 152.076, 82.203
Angle α, β, γ (deg.)90.00, 104.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLYGLY1AA12 - 50612 - 506
21HISHISGLYGLY1BB12 - 50612 - 506
12MLGMLGMLGMLG4AD601
22MLGMLGMLGMLG4BF601

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Components

#1: Protein AMINE OXIDASE [FLAVIN-CONTAINING] A / MONOAMINE OXIDASE TYPE A / MAO-A


Mass: 59759.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P21397, 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-MLG / N-[3-(2,4-DICHLOROPHENOXY)PROPYL]-N-METHYL-N-PROP-2-YNYLAMINE / N-METHYL-N-PROPARGYL-3-(2,4-DICHLOROPHENOXY)PROPYLAMINE


Mass: 272.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15Cl2NO / Comment: antidepressant, inhibitor*YM
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: 4.01 Å3/Da / Density % sol: 50 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 5% PEG 6000, 100 MM NACITRATE, 100 MM LISULPHATE, 50 MM KPI PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→15 Å / Num. obs: 27718 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.01
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.04 / % possible all: 67.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2Q

1s2q


Resolution: 3.15→15 Å / Cor.coef. Fo:Fc: 0.815 / Cor.coef. Fo:Fc free: 0.743 / SU B: 55.597 / SU ML: 0.458 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.584
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.33 1484 5.1 %RANDOM
Rwork0.268 ---
obs0.271 27718 90.5 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 37.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.24 Å2
2---0.35 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 3.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7760 0 140 0 7900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.741.97211000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6685976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27124.068354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.232151364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0251544
X-RAY DIFFRACTIONr_chiral_restr0.110.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.24997
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.340.25563
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3071.54959
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.49527850
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.90733650
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2814.53150
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3880tight positional0.050.05
17medium positional0.240.5
3880tight thermal0.110.5
17medium thermal0.852
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 56
Rwork0.241 1285
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75240.14160.24246.0013-1.35384.2722-0.06130.11240.14980.07080.69040.3322-0.6246-0.3813-0.6291-0.5735-0.00910.1211-0.27410.0651-0.336318.1315122.767754.2256
22.6669-0.4333-1.16285.86520.75923.1602-0.3827-0.0717-0.150.20250.5654-0.26610.57280.3189-0.1827-0.3079-0.0078-0.1762-0.2864-0.0656-0.504843.0373-0.249118.0239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 506
2X-RAY DIFFRACTION2B12 - 506

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