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Yorodumi- PDB-5k0f: Crystal Structure of COMT in complex with 5-[5-[1-(4-methoxypheny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k0f | ||||||
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Title | Crystal Structure of COMT in complex with 5-[5-[1-(4-methoxyphenyl)ethyl]-1H-pyrazol-3-yl]-2,4-dimethyl-1,3-thiazole | ||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL | ||||||
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 / : / : / catechol O-methyltransferase / developmental process / renin secretion into blood stream / renal filtration / renal albumin absorption / dopamine secretion / S-adenosylmethionine metabolic process / negative regulation of dopamine 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 / response to angiotensin / cellular response to cocaine / estrogen metabolic process / response to food / exploration behavior / cholesterol efflux / response to temperature stimulus / response to pain / 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 / multicellular organismal response to stress / behavioral fear response / response to amphetamine / response to organic substance / learning / kidney development / female pregnancy / response to cytokine / 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 / postsynapse / postsynaptic membrane / 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 / Resolution: 1.81 Å | ||||||
Authors | Ehler, A. / Rodriguez-Sarmiento, R.M. / Rudolph, M.G. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2016 Title: Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket. Authors: Lerner, C. / Jakob-Roetne, R. / Buettelmann, B. / Ehler, A. / Rudolph, M. / Rodriguez Sarmiento, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k0f.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k0f.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/5k0f ftp://data.pdbj.org/pub/pdb/validation_reports/k0/5k0f | HTTPS FTP |
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-Related structure data
Related structure data | 5k03C 5k05C 5k09C 5k0bC 5k0cC 5k0gC 5k0jC 5k0lC 5k0nC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24475.990 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #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: 2.91 Å3/Da / Density % sol: 57.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→47.541 Å / Num. obs: 52148 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.48 % / Biso Wilson estimate: 36.068 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.81→47.541 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 94.3 Å2 / Biso mean: 31.2499 Å2 / Biso min: 15.7 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.81→47.541 Å
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