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Yorodumi- PDB-4a79: Crystal structure of human monoamine oxidase B (MAO B) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a79 | ||||||
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Title | Crystal structure of human monoamine oxidase B (MAO B) in complex with pioglitazone | ||||||
Components | AMINE OXIDASE [FLAVIN-CONTAINING] B | ||||||
Keywords | OXIDOREDUCTASE / ANTI-DIABETES DRUG / PARKINSON'S DISEASE / NEURODEGENERATION | ||||||
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: 1.89 Å | ||||||
Authors | Binda, C. / Aldeco, M. / Geldenhuys, W.J. / Tortorici, M. / Mattevi, A. / Edmondson, D.E. | ||||||
Citation | Journal: Acs Med. Chem. Lett. / Year: 2012 Title: Molecular Insights Into Human Monoamine Oxidase B Inhibition by the Glitazone Anti-Diabetes Drugs Authors: Binda, C. / Aldeco, M. / Geldenhuys, W.J. / Tortorici, M. / Mattevi, A. / Edmondson, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a79.cif.gz | 224.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a79.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/4a79 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a79 | HTTPS FTP |
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-Related structure data
Related structure data | 4a7aC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.53053, -0.49226, -0.69008), Vector: |
-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) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71 / References: UniProt: P27338, monoamine oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | FAD (FLAVIN-ADENINE DINUCLEOTI | |
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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: 2.72 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 12% PEG 4000, 100 MM ADA PH 6.5, 70 MM LITHIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39 Å / Num. obs: 102915 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V5Z Resolution: 1.89→38.28 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.308 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.877 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→38.28 Å
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Refine LS restraints |
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