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Yorodumi- PDB-5p9n: humanized rat COMT in complex with 5-(4-fluorophenyl)-2,3-dihydro... -
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-Basic information
Entry | Database: PDB / ID: 5p9n | ||||||
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Title | humanized rat COMT in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[[3-[hydroxy-(1-methylindazol-5-yl)methyl]phenyl]methyl]benzamide at 1.17A | ||||||
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 / 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: 1.17 Å | ||||||
Authors | Ehler, A. / Jakob-Roetne, R. / Rudolph, M.G. | ||||||
Citation | Journal: To be published Title: Crystal Structure of a COMT complex Authors: Lerner, C. / Jakob-Roetne, R. / Groebke-Zbinden, K. / Buettelmann, B. / 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 | 5p9n.cif.gz | 120.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5p9n.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 5p9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/5p9n ftp://data.pdbj.org/pub/pdb/validation_reports/p9/5p9n | HTTPS FTP |
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-Group deposition
ID | G_1002014 (21 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: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264 / 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) / Strain (production host): BL21(DE3) / References: UniProt: P22734, catechol O-methyltransferase |
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-Non-polymers , 8 types, 234 molecules
#2: Chemical | ChemComp-MG / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-NHE / | #5: Chemical | ChemComp-D1D / ( | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-7JE / | #8: Chemical | ChemComp-8JE / | #9: 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: 44.25 % |
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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: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→44.9 Å / Num. obs: 73568 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.22 % / Biso Wilson estimate: 17.07 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.17→1.2 Å / Rmerge(I) obs: 1.278 / Mean I/σ(I) obs: 1.1 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INHOUSE MODEL Resolution: 1.17→44.9 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.322 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: BOTH ENANTIOMERS BIND, SEE ALTERNATE CONF FOR LIGAND SHORT 2.3A H-BOND OF ONE OH TO GLU SIDE-CHAIN SUPPORTED BY DENSITY POSSIBLY SEVERAL SLIGHTLY DIFFERENT CONFORMATIONS OF GLU BUT NOT ...Details: BOTH ENANTIOMERS BIND, SEE ALTERNATE CONF FOR LIGAND SHORT 2.3A H-BOND OF ONE OH TO GLU SIDE-CHAIN SUPPORTED BY DENSITY POSSIBLY SEVERAL SLIGHTLY DIFFERENT CONFORMATIONS OF GLU BUT NOT MODELED. HYDROGENS HAVE BEEN USED
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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: 13.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.17→44.9 Å
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