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Yorodumi- PDB-2xfo: tranylcypromine-inhibited human monoamine oxidase B Ile199Ala mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xfo | ||||||
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Title | tranylcypromine-inhibited human monoamine oxidase B Ile199Ala mutant in complex with 2-(2-benzofuranyl)-2-imidazoline | ||||||
Components | Amine oxidase [flavin-containing] B | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information Biogenic amines are oxidatively deaminated to aldehydes by MAOA and MAOB / monoamine oxidase activity / monoamine oxidase / 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 activity / monoamine oxidase / 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 / dopamine catabolic process / primary methylamine oxidase activity / 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 | 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 | 2xfo.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xfo.ent.gz | 173.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xfo_validation.pdf.gz | 979.8 KB | Display | wwPDB validaton report |
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Full document | 2xfo_full_validation.pdf.gz | 994.8 KB | Display | |
Data in XML | 2xfo_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 2xfo_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/2xfo ftp://data.pdbj.org/pub/pdb/validation_reports/xf/2xfo | HTTPS FTP |
-Related structure data
Related structure data | 2xcgC 2xfnC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58795.652 Da / Num. of mol.: 2 / Mutation: 199A 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, 309 molecules
#2: Chemical | ChemComp-FA8 / [[( | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FAD / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEEREDNonpolymer details | TRANYLCYPROMINE (TRA): CAK ATOM OF TRA IS COVALENTLY ATTACHED TO C4A ATOM OF FAD FLAVIN-ADENINE ...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: 2.72 Å3/Da / Density % sol: 54.78 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Type: ESRF / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 69410 / % possible obs: 95.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.8 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OJB 1ojb Resolution: 2.1→65.27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Refinement step | Cycle: LAST / Resolution: 2.1→65.27 Å
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