+Open data
-Basic information
Entry | Database: PDB / ID: 4pyo | ||||||
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Title | Humanized rat COMT bound to SAH, semi-holo form | ||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE | ||||||
Function / homology | Function and homology information Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process / response to salt / catechol O-methyltransferase activity / renal sodium excretion / : / : / renin secretion into blood stream / developmental process / catechol O-methyltransferase / renal filtration / renal albumin absorption / dopamine secretion / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / habituation / artery development / catecholamine metabolic process / short-term memory / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / cholesterol efflux / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / response to pain / response to temperature stimulus / dopamine metabolic process / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / response to inorganic substance / behavioral fear response / multicellular organismal response to stress / response to amphetamine / learning / kidney development / response to organic substance / response to cytokine / female pregnancy / negative regulation of smooth muscle cell proliferation / multicellular organism growth / visual learning / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / cell body / gene expression / methylation / postsynaptic membrane / postsynapse / response to oxidative stress / vesicle / response to lipopolysaccharide / dendritic spine / response to hypoxia / learning or memory / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Mapping the conformational space accessible to catechol-O-methyltransferase. Authors: Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pyo.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pyo.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 4pyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/4pyo ftp://data.pdbj.org/pub/pdb/validation_reports/py/4pyo | HTTPS FTP |
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-Related structure data
Related structure data | 4p7fC 4p7gC 4p7jC 4p7kC 4pyiC 4pyjC 4pykC 4pylC 4pymC 4pynC 4pyqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24694.332 Da / Num. of mol.: 2 / Mutation: M134I, Y138C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli (E. coli) / References: UniProt: P22734, catechol O-methyltransferase #2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-MG / | #5: 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: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 293 K / Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2011 |
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→45.9 Å / Num. obs: 31280 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.11322 / Net I/σ(I): 10.2398 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.5045 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.88 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 29.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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