+Open data
-Basic information
Entry | Database: PDB / ID: 2vrl | ||||||
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Title | Structure of human MAO B in complex with benzylhydrazine | ||||||
Components | AMINE OXIDASE [FLAVIN-CONTAINING] B | ||||||
Keywords | OXIDOREDUCTASE / FAD / FLAVIN / MEMBRANE / HYDRAZINE / ACETYLATION / FLAVOPROTEIN / MITOCHONDRION / TRANSMEMBRANE / INHIBITOR BINDING / MEMBRANE PROTEIN / MONOAMINE OXIDASE | ||||||
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: 2.4 Å | ||||||
Authors | Binda, C. / Wang, J. / Li, M. / Hubalek, F. / Mattevi, A. / Edmondson, D.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural and Mechanistic Studies of Arylalkylhydrazine Inhibition of Human Monoamine Oxidases a and B Authors: Binda, C. / Wang, J. / Li, M. / Hubalek, F. / 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 | 2vrl.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrl.ent.gz | 175 KB | Display | PDB format |
PDBx/mmJSON format | 2vrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrl ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.5318, -0.495, -0.6871), 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) / References: UniProt: P27338, monoamine oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE COMPOUND USED FOR CO-CRYSTALLIZATION IS THE MAO B INHIBITOR BENZYLHYDRAZINE (BZZ), WHICH IS ...THE COMPOUND USED FOR CO-CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55.25 % / Description: NONE |
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Crystal grow | Details: 12% PEG4000 100MM ADA PH 6.5 70MM LITHIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 46894 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.169 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.25 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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