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Yorodumi- PDB-5p95: rat catechol O-methyltransferase in complex with N-[5-(6-aminopur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5p95 | |||||||||
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Title | rat catechol O-methyltransferase in complex with N-[5-(6-aminopurin-9-yl)pentyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide at 1.30A | |||||||||
Components | Catechol O-methyltransferaseCatechol-O-methyltransferase | |||||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION | |||||||||
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 / catechol O-methyltransferase activity ...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 / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal filtration / renin secretion into blood stream / dopamine secretion / renal albumin absorption / negative regulation of dopamine metabolic process / response to salt / habituation / artery development / catecholamine metabolic process / S-adenosylmethionine metabolic process / short-term memory / cerebellar cortex morphogenesis / cellular response to phosphate starvation / 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 / exploration behavior / response to food / cholesterol efflux / response to temperature stimulus / response to pain / response to corticosterone / dopamine metabolic process / glycogen metabolic process / prostaglandin metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / : / behavioral fear response / multicellular organismal response to stress / response to amphetamine / : / learning / kidney development / response to cytokine / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / response to toxic substance / memory / 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 / learning or memory / response to hypoxia / response to xenobiotic stimulus / axon / glutamatergic synapse / dendrite / 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. / Lerner, C. / Rudolph, M.G. | |||||||||
Citation | Journal: To be published Title: Crystal Structure of a COMT complex Authors: Lerner, C. / 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 | 5p95.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5p95.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 5p95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/5p95 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/5p95 | HTTPS FTP |
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-Group deposition
ID | G_1002010 (10 entries) |
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Title | Crystal Structure of COMT complex |
Type | undefined |
Description | Crystal Structure of COMT complex |
-Related structure data
Similar structure data |
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-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, RESIDUES 44-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22734, catechol O-methyltransferase |
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-Non-polymers , 7 types, 350 molecules
#2: Chemical | ChemComp-MG / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-77G / | #5: Chemical | ChemComp-D1D / ( | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-NHE / | #8: 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: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9 |
-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: Jun 15, 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→40.42 Å / Num. obs: 54119 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.85 % / Biso Wilson estimate: 16.69 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.47 |
Reflection shell | Resolution: 1.3→1.33 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.46 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INHOUSE MODEL Resolution: 1.3→40.42 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.31 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ADENINE PART HAS TWO CONFORMATIONS THAT ARE COUPLED TO THE NEARBY TRP. OXIDIZED DTE AND CHES BUFFER ARE SUPERIMPOSED NEAR FLUOROPHENYL MOIETY. SEVERAL PARTIALLY OCCUPIED WATER MOLECULES MODELED IN BINDING SITE
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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: 9.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→40.42 Å
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Refine LS restraints |
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