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Yorodumi- PDB-6rkp: Crystal structure of human monoamine oxidase B in complex with st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rkp | ||||||
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Title | Crystal structure of human monoamine oxidase B in complex with styrylpiperidine analogue 84 | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | FLAVOPROTEIN / monoamine oxidase / drug target / neurodegeneration / flavin / isomer / mitochondrial membrane | ||||||
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: 1.7 Å | ||||||
Authors | Iacovino, L.G. / Knez, D. / Colettis, N. / Sova, M. / Pislar, A. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. ...Iacovino, L.G. / Knez, D. / Colettis, N. / Sova, M. / Pislar, A. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. / Trontelj, J. / Kos, J. / Marder, N.M. / Gobec, S. / Binda, C. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Stereoselective Activity of 1-Propargyl-4-styrylpiperidine-like Analogues That Can Discriminate between Monoamine Oxidase Isoforms A and B. Authors: Knez, D. / Colettis, N. / Iacovino, L.G. / Sova, M. / Pislar, A. / Konc, J. / Lesnik, S. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. / Trontelj, J. / Kos, J. / ...Authors: Knez, D. / Colettis, N. / Iacovino, L.G. / Sova, M. / Pislar, A. / Konc, J. / Lesnik, S. / Higgs, J. / Kamecki, F. / Mangialavori, I. / Dolsak, A. / Zakelj, S. / Trontelj, J. / Kos, J. / Binda, C. / Marder, M. / Gobec, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rkp.cif.gz | 232.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rkp.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/6rkp ftp://data.pdbj.org/pub/pdb/validation_reports/rk/6rkp | HTTPS FTP |
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-Related structure data
Related structure data | 6rkbC 6rleC 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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-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, 777 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / 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: ESRF / Beamline: ID30B / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.71 Å / Num. obs: 141411 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 1.666 / Num. unique obs: 6932 / CC1/2: 0.503 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v5z Resolution: 1.7→47.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.264 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / 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: 23.534 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→47.7 Å
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Refine LS restraints |
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