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Yorodumi- PDB-5mrl: Crystal structure of human monoamine oxidase B (MAO B) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mrl | ||||||
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Title | Crystal structure of human monoamine oxidase B (MAO B) in complex with N(Furan2ylmethyl)Nmethylprop2yn1amine (F2MPA) | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | OXIDOREDUCTASE / monoamine oxidase / neurodegeneration / inhibitor / enzyme | ||||||
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: 2.42 Å | ||||||
Authors | Binda, C. / De Deurwaerdere, P. / Corne, R. / Leone, C. / Valeri, A. / Valoti, M. / Ramsay, R.R. / Fall, Y. / Marco-Contelles, J. | ||||||
Funding support | Italy, 1items
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Citation | Journal: ACS Chem Neurosci / Year: 2017 Title: Comparative Analysis of the Neurochemical Profile and MAO Inhibition Properties of N-(Furan-2-ylmethyl)-N-methylprop-2-yn-1-amine. Authors: De Deurwaerdere, P. / Binda, C. / Corne, R. / Leone, C. / Valeri, A. / Valoti, M. / Ramsay, R.R. / Fall, Y. / Marco-Contelles, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrl.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrl.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrl ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrl | HTTPS FTP |
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-Related structure data
Related structure data | 2v5zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 / Production host: Komagataella 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: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG4000, ADA, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→113 Å / Num. obs: 48068 / % possible obs: 98.4 % / Redundancy: 7.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 4 / CC1/2: 0.781 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v5z Resolution: 2.42→113 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.871 / SU B: 7.003 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.341 Å2
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Refinement step | Cycle: 1 / Resolution: 2.42→113 Å
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Refine LS restraints |
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