+Open data
-Basic information
Entry | Database: PDB / ID: 4p7k | ||||||
---|---|---|---|---|---|---|---|
Title | Rat COMT in complex with sinefungin | ||||||
Components | Catechol O-methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / S-ADENOSYL-L-METHIONINE / 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 / cellular response to phosphate starvation / norepinephrine metabolic process / dopamine catabolic process / glomerulus development / fear response / 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 corticosterone / prostaglandin metabolic process / response to pain / 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 / negative regulation of smooth muscle cell proliferation / learning / kidney development / response to cytokine / female pregnancy / regulation of blood pressure / visual learning / multicellular organism growth / response to organic cyclic compound / response to toxic substance / memory / cognition / response to wounding / response to estrogen / gene expression / cell body / postsynaptic membrane / methylation / vesicle / response to oxidative stress / postsynapse / response to lipopolysaccharide / learning or memory / dendritic spine / 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 / Resolution: 1.22 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4p7k.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4p7k.ent.gz | 127.6 KB | Display | PDB format |
PDBx/mmJSON format | 4p7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p7k_validation.pdf.gz | 739.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4p7k_full_validation.pdf.gz | 740 KB | Display | |
Data in XML | 4p7k_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4p7k_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/4p7k ftp://data.pdbj.org/pub/pdb/validation_reports/p7/4p7k | HTTPS FTP |
-Related structure data
Related structure data | 4p7fC 4p7gC 4p7jC 4pyiC 4pyjC 4pykC 4pylC 4pymC 4pynC 4pyoC 4pyqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: UNP 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) / References: UniProt: P22734, catechol O-methyltransferase |
---|
-Non-polymers , 5 types, 322 molecules
#2: Chemical | ChemComp-SFG / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-TLA / | ||||
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 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: 1.22→31.7 Å / Num. obs: 48898 / % possible obs: 75.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.03518 / Net I/σ(I): 28.7269 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.34407 / Mean I/σ(I) obs: 2.4205 / % possible all: 13.8 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1439) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.22→31.7 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 15.14 / Phase error: 14.82 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→31.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|