+Open data
-Basic information
Entry | Database: PDB / ID: 2cl5 | ||||||
---|---|---|---|---|---|---|---|
Title | Catechol-O-methyltransferase in complex with an inhibitor | ||||||
Components | CATECHOL O-METHYLTRANSFERASECatechol-O-methyltransferase | ||||||
Keywords | TRANSFERASE / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / NEUROTRANSMITTER DEGRADATION / CATECHOL-O-METHYLTRANSFERASE / PHOSPHORYLATION / METHYLTRANSFERASE / SIGNAL-ANCHOR / TRANSMEMBRANE / COMT INHIBITOR / MEMBRANE / MAGNESIUM / METAL-BINDING | ||||||
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: 1.6 Å | ||||||
Authors | Palma, P.N. / Rodrigues, M.L. / Archer, M. / Bonifacio, M.J. / Loureiro, A.I. / Learmonth, D.A. / Carrondo, M.A. / Soares-Da-Silva, P. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2006 Title: Comparative Study of Ortho- and Meta-Nitrated Inhibitors of Catechol-O-Methyltransferase: Interactions with the Active Site and Regioselectivity of O-Methylation. Authors: Palma, P.N. / Rodrigues, M.L. / Archer, M. / Bonifacio, M.J. / Loureiro, A.I. / Learmonth, D.A. / Carrondo, M.A. / Soares-Da-Silva, P. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Catechol-O-Methyltransferase-Inhibitor Complex Authors: Rodrigues, M.L. / Bonifacio, M.J. / Soares-Da-Silva, P. / Carrondo, M.A. / Archer, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cl5.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cl5.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/2cl5 ftp://data.pdbj.org/pub/pdb/validation_reports/cl/2cl5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1h1dS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24772.400 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: QIAGEN MIDI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22734, catechol O-methyltransferase |
---|
-Non-polymers , 6 types, 564 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MES / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
---|---|
Crystal grow | pH: 6.5 / Details: 8% PEG6K, 0.1 M MES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→24.42 Å / Num. obs: 67299 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.6→1.64 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1D Resolution: 1.6→62.02 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.37 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15.37 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→62.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|