+Open data
-Basic information
Entry | Database: PDB / ID: 4pym | ||||||
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Title | humanized rat apo-COMT bound to sulphate | ||||||
Components | Catechol O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL 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 / catechol-containing compound metabolic process / catecholamine catabolic 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 / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / renal filtration / developmental process / renin secretion into blood stream / dopamine secretion / negative regulation of dopamine metabolic process / renal albumin absorption / catecholamine metabolic process / habituation / artery development / response to salt / short-term memory / S-adenosylmethionine metabolic process / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / 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 / prostaglandin metabolic process / glycogen metabolic process / dopamine 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 / response to cytokine / kidney development / 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 / gene expression / cell body / postsynapse / methylation / postsynaptic membrane / vesicle / response to oxidative stress / 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: 1.19 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 | 4pym.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pym.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 4pym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pym_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 4pym_full_validation.pdf.gz | 427.4 KB | Display | |
Data in XML | 4pym_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4pym_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/4pym ftp://data.pdbj.org/pub/pdb/validation_reports/py/4pym | HTTPS FTP |
-Related structure data
Related structure data | 4p7fC 4p7gC 4p7jC 4p7kC 4pyiC 4pyjC 4pykC 4pylC 4pynC 4pyoC 4pyqC 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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Unit cell |
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-Components
#1: Protein | Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: unp 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) / References: UniProt: P22734, catechol O-methyltransferase |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.16 Å3/Da / Density % sol: 43.03 % |
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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: Mar 29, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→30.7 Å / Num. obs: 68613 / % possible obs: 98.7 % |
Reflection shell | Resolution: 1.19→1.23 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 1.078 / % possible all: 97.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→30.77 Å / SU ML: 0.12 / σ(F): 14.6 / Phase error: 17.19 / 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: 1.19→30.77 Å
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Refine LS restraints |
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LS refinement shell |
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