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- PDB-5k0n: Crystal Structure of COMT in complex with 4-[5-[1-(4-methoxypheny... -

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Basic information

Entry
Database: PDB / ID: 5k0n
TitleCrystal Structure of COMT in complex with 4-[5-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-3-yl]-1,3-dimethylpyrazole
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL
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 O-methyltransferase activity / 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 O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / dopamine secretion / renin secretion into blood stream / negative regulation of dopamine metabolic process / fear response / catecholamine metabolic process / renal albumin absorption / artery development / habituation / short-term memory / cerebellar cortex morphogenesis / S-adenosylmethionine metabolic process / response to salt / dopamine catabolic process / cellular response to phosphate starvation / glomerulus development / norepinephrine metabolic process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / response to stress / response to food / exploration behavior / response to temperature stimulus / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / response to pain / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to cytokine / kidney development / learning / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynaptic membrane / vesicle / postsynapse / methylation / 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
Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6P0 / : / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.99 Å
AuthorsEhler, A. / Rodriguez-Sarmiento, R.M.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket.
Authors: Lerner, C. / Jakob-Roetne, R. / Buettelmann, B. / Ehler, A. / Rudolph, M. / Rodriguez Sarmiento, R.M.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,10824
Polymers98,2534
Non-polymers2,85520
Water11,115617
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2046
Polymers24,5631
Non-polymers6415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1425
Polymers24,5631
Non-polymers5794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3496
Polymers24,5631
Non-polymers7865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4127
Polymers24,5631
Non-polymers8486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.023, 69.890, 104.102
Angle α, β, γ (deg.)90.000, 94.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Catechol O-methyltransferase


Mass: 24563.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 6 types, 637 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Chemical
ChemComp-6P0 / 5-[1-(4-methoxyphenyl)cyclopropyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole


Mass: 308.378 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H20N4O
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS-HCL pH 7, 1.8 M ammonium sulfate, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.99→47.19 Å / Num. obs: 75495 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 35.606 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.61
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.99-2.041.091.12198.9
2.04-2.10.9221.38198.8
2.1-2.160.7441.83199
2.16-2.220.5882.3198.8
2.22-2.30.4682.89199.4
2.3-2.380.3663.58199.3
2.38-2.470.2944.34199.1
2.47-2.570.2455.21199.3
2.57-2.680.2056.27199.4
2.68-2.810.177.39199.8
2.81-2.970.1329.07199.6
2.97-3.150.09910.98199.4
3.15-3.360.0714.01199.3
3.36-3.630.05218.4199.3
3.63-3.980.04421.33199.3
3.98-4.450.03923.92198.9
4.45-5.140.03524.62199
5.14-6.290.03923.37199.4
6.29-8.90.03123.97198.4
8.90.02428.18197.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.99→45.418 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.2325 3889 5.15 %
Rwork0.1838 --
obs0.1862 75495 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.36 Å2 / Biso mean: 31.0817 Å2 / Biso min: 15.38 Å2
Refinement stepCycle: final / Resolution: 1.99→45.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6876 0 186 617 7679
Biso mean--29.65 38.57 -
Num. residues----880

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