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

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Basic information

Entry
Database: PDB / ID: 2bxr
TitleHuman Monoamine Oxidase A in complex with Clorgyline, Crystal Form A
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 / 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 / : / 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
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 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 1.2Oct 2, 2019Group: Data collection / Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)143.493, 109.599, 81.329
Angle α, β, γ (deg.)90.00, 95.18, 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 - 46412 - 464
21HISHISGLYGLY1BB12 - 46412 - 464
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
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: 2.66 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 6% PEG 6000, 100 MM LISULPHATE, 100 MM NACITRATE, 50 MM KPI PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorDate: Feb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 23085 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.01
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.52 / % possible all: 97.3

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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→87.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 37.83 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.411
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1245 5.1 %RANDOM
Rwork0.192 ---
obs0.195 23085 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.82 Å20 Å21.86 Å2
2---3.67 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 3→87.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7046 0 140 0 7186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9749998
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41423.889324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.175151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8941542
X-RAY DIFFRACTIONr_chiral_restr0.1030.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025536
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.23710
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.25003
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3381.54480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.58527100
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08433336
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6094.52898
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
3523tight positional0.040.05
17medium positional0.150.5
3523tight thermal0.090.5
17medium thermal0.422
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.373 99
Rwork0.312 1684
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)
11.3509-0.72930.22734.4522-1.04335.1016-0.10680.0928-0.0408-0.29350.1880.11340.6624-0.4846-0.0812-0.301-0.11510.0822-0.31310.0057-0.337630.72631.77445.9853
22.27031.0517-0.7295.12260.00524.71220.0368-0.10280.05550.01140.19080.2542-0.5209-0.4453-0.2276-0.31410.093-0.0989-0.29250.0671-0.326627.5055-25.519833.8195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 464
2X-RAY DIFFRACTION2B12 - 464

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