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Yorodumi- PDB-7b0z: Crystal Structure of human monoamine oxidase B in complex with (E... -
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-Basic information
Entry | Database: PDB / ID: 7b0z | ||||||
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Title | Crystal Structure of human monoamine oxidase B in complex with (E)-3-phenyl-1-(4-(trifluoromethyl)phenyl)prop-2-en-1-one | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | FLAVOPROTEIN / monoamine oxidase / drug target / neurodegeneration / flavin / chalcone / mitochondrial membrane | ||||||
Function / homology | Function and homology information Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity ...Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase / monoamine oxidase activity / phenylethylamine catabolic process / positive regulation of dopamine metabolic process / response to aluminum ion / negative regulation of serotonin secretion / response to selenium ion / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / dopamine catabolic process / 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 / neuronal cell body / dendrite / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Iacovino, L.G. / Binda, C. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Promising Non-cytotoxic Monosubstituted Chalcones to Target Monoamine Oxidase-B. Authors: Iacovino, L.G. / Pinzi, L. / Facchetti, G. / Bortolini, B. / Christodoulou, M.S. / Binda, C. / Rastelli, G. / Rimoldi, I. / Passarella, D. / Di Paolo, M.L. / Dalla Via, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b0z.cif.gz | 228.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0z.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b0z_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7b0z_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7b0z_validation.xml.gz | 44 KB | Display | |
Data in CIF | 7b0z_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0z ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0z | HTTPS FTP |
-Related structure data
Related structure data | 7b0vC 2v5zS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 715 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 53.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 4000, lithium sulphate, ADA buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.3 Å / Num. obs: 69971 / % possible obs: 99.92 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.1→2.15 Å / Num. unique obs: 5125 / CC1/2: 0.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v5z Resolution: 2.1→47.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.778 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.69 Å2 / Biso mean: 19.793 Å2 / Biso min: 7.92 Å2
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Refinement step | Cycle: final / Resolution: 2.1→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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