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Yorodumi- PDB-2xcg: Tranylcypromine-inhibited human monoamine oxidase B in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xcg | ||||||
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Title | Tranylcypromine-inhibited human monoamine oxidase B in complex with 2- (2-benzofuranyl)-2-imidazoline | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / MAOB / MITOCHONDRION / TRANSMEMBRANE | ||||||
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: 1.9 Å | ||||||
Authors | Bonivento, D. / Milczek, E.M. / McDonald, G.R. / Binda, C. / Holt, A. / Edmondson, D.E. / Mattevi, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2010 Title: Potentiation of ligand binding through cooperative effects in monoamine oxidase B. Authors: Bonivento, D. / Milczek, E.M. / McDonald, G.R. / Binda, C. / Holt, A. / 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 | 2xcg.cif.gz | 230.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xcg.ent.gz | 184 KB | Display | PDB format |
PDBx/mmJSON format | 2xcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xcg ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xcg | HTTPS FTP |
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-Related structure data
Related structure data | 2xfnC 2xfoC 2xfpC 2xfqC 2xfuC 1ojb C: citing same article (ref.) 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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2 |
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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, 762 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | TRANYLCYPR |
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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: 2.56 Å3/Da / Density % sol: 51.63 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: PEG 4000 12%, LISO4 70MM, ADA 0.1M PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 100933 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJB 1ojb Resolution: 1.9→46.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.149 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / 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: 13.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.98 Å
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Refine LS restraints |
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