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Yorodumi- PDB-3hvk: Rat catechol O-methyltransferase in complex with a catechol-type,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hvk | ||||||
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Title | Rat catechol O-methyltransferase in complex with a catechol-type, purine-containing bisubstrate inhibitor - humanized form | ||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / Alternative initiation / Catecholamine metabolism / Cell membrane / Magnesium / Membrane / Metal-binding / Phosphoprotein / S-adenosyl-L-methionine / Signal-anchor / Transmembrane | ||||||
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: 1.3 Å | ||||||
Authors | Ehler, A. / Schlatter, D. / Stihle, M. / Benz, J. / Rudolph, M.G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009 Title: Molecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor. Authors: Ellermann, M. / Jakob-Roetne, R. / Lerner, C. / Borroni, E. / Schlatter, D. / Roth, D. / Ehler, A. / Rudolph, M.G. / Diederich, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hvk.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hvk.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 3hvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/3hvk ftp://data.pdbj.org/pub/pdb/validation_reports/hv/3hvk | HTTPS FTP |
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-Related 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, 1 molecules A
#1: Protein | Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, UNP RESIDUES 44-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: LIVER / Plasmid: pDS56/RBSII / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) / References: UniProt: P22734, catechol O-methyltransferase |
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-Non-polymers , 5 types, 245 molecules
#2: Chemical | ChemComp-MG / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-NHE / | #5: Chemical | ChemComp-719 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: 1.4M ammonium sulfate, 0.1M CHES pH 8.9, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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: May 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→32.1 Å / Num. obs: 52192 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1757 / Rsym value: 0.467 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.539 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.164 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→31.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.298→1.332 Å / Total num. of bins used: 20
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