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Yorodumi- PDB-1s3b: Crystal structure of MAOB in complex with N-methyl-N-propargyl-1(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s3b | ||||||
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Title | Crystal structure of MAOB in complex with N-methyl-N-propargyl-1(R)-aminoindan | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | OXIDOREDUCTASE / human monoamine oxidase / inhibitor binding / rasagiline / enantioselectivity / flavin | ||||||
Function / homology | Function and homology information Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / aliphatic amine oxidase activity / monoamine oxidase activity / monoamine oxidase / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / primary amine oxidase activity / negative regulation of serotonin secretion / response to aluminum ion / response to selenium ion / : / dopamine catabolic process / primary-amine oxidase / mitochondrial envelope / hydrogen peroxide biosynthetic process / response to corticosterone / substantia nigra development / response to toxic substance / flavin adenine dinucleotide binding / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / response to xenobiotic stimulus / dendrite / neuronal cell body / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Binda, C. / Hubalek, F. / Li, M. / Herzig, Y. / Sterling, J. / Edmondson, D.E. / Mattevi, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Crystal Structures of Monoamine Oxidase B in Complex with Four Inhibitors of the N-Propargylaminoindan Class. Authors: Binda, C. / Li, M. / Herzig, Y. / Sterling, J. / Edmondson, D.E. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s3b.cif.gz | 222.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s3b.ent.gz | 184.8 KB | Display | PDB format |
PDBx/mmJSON format | 1s3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/1s3b ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s3b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
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Details | The biological assembly is a homodimer that is all contained in the asymmetric unit |
-Components
#1: Protein | Mass: 58837.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAOB / Plasmid: pPIC3.5K / Production host: Pichia pastoris (fungus) / References: UniProt: P27338, monoamine oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG4000, lithium sulphate, ADA buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2003 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→15 Å / Num. all: 147574 / Num. obs: 147574 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.65→5.22 Å / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.778 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.244 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3910 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20 /
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