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Basic information

Entry
Database: PDB / ID: 1o5w
TitleThe structure basis of specific recognitions for substrates and inhibitors of rat monoamine oxidase A
ComponentsAmine oxidase [flavin-containing] A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


phenylethylamine metabolic process / Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / : / Metabolism of serotonin / monoamine oxidase / positive regulation of signal transduction / Norepinephrine Neurotransmitter Release Cycle / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / catecholamine catabolic process ...phenylethylamine metabolic process / Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / : / Metabolism of serotonin / monoamine oxidase / positive regulation of signal transduction / Norepinephrine Neurotransmitter Release Cycle / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / catecholamine catabolic process / serotonin metabolic process / dopamine catabolic process / serotonin binding / primary amine oxidase activity / flavin adenine dinucleotide binding / mitochondrial outer membrane / membrane => GO:0016020
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #130 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / FAD/NAD(P)-binding domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #130 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helix non-globular / 3-Layer(bba) Sandwich / Special / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMa, J. / Yoshimura, M. / Yamashita, E. / Nakagawa, A. / Ito, A. / Tsukihara, T.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of rat monoamine oxidase a and its specific recognitions for substrates and inhibitors.
Authors: Ma, J. / Yoshimura, M. / Yamashita, E. / Nakagawa, A. / Ito, A. / Tsukihara, T.
History
DepositionOct 6, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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] A
B: Amine oxidase [flavin-containing] A
C: Amine oxidase [flavin-containing] A
D: Amine oxidase [flavin-containing] A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,68612
Polymers242,4564
Non-polymers4,2318
Water0
1
A: Amine oxidase [flavin-containing] A
B: Amine oxidase [flavin-containing] A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3436
Polymers121,2282
Non-polymers2,1154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-64 kcal/mol
Surface area38150 Å2
MethodPISA
2
C: Amine oxidase [flavin-containing] A
D: Amine oxidase [flavin-containing] A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,3436
Polymers121,2282
Non-polymers2,1154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-62 kcal/mol
Surface area38660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.560, 157.560, 257.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Amine oxidase [flavin-containing] A / Monoamine oxidase / MAO-A


Mass: 60613.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: YEp51 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: P21396, monoamine oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / 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 / Clorgiline


Mass: 272.170 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H15Cl2NO / Comment: antidepressant, inhibitor*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.31 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 59281

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→16.19 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2848495.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2684 5 %RANDOM
Rwork0.22 ---
obs0.242 53285 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7025 Å2 / ksol: 0.240749 e/Å3
Displacement parametersBiso mean: 93.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.58 Å20 Å20 Å2
2---3.58 Å20 Å2
3---7.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.2→16.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16176 0 280 0 16456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 396 4.5 %
Rwork0.352 8388 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FAD_XPLOR_PARAMFAD_XPLOR_TOP
X-RAY DIFFRACTION3CLG_PARAMCLG_TOP
X-RAY DIFFRACTION4PARAM.FAD_CYSTOPH.FAD_CYS
X-RAY DIFFRACTION5PARAM.FAD_CLGTOPH.FAD_CLG

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