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- PDB-5k0l: Crystal Structure of COMT in complex with 5-[5-[1-(4-methoxypheny... -

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Basic information

Entry
Database: PDB / ID: 5k0l
TitleCrystal Structure of COMT in complex with 5-[5-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-3-yl]-2,4-dimethyl-1,3-thiazole
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL
Function / homology
Function and homology information


positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / 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 / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / habituation / artery development / short-term memory / cerebellar cortex morphogenesis / response to salt / dopamine catabolic process / glomerulus development / norepinephrine metabolic process / fear response / synaptic transmission, dopaminergic / cellular response to phosphate starvation / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / cholesterol efflux / response to food / prostaglandin metabolic process / response to corticosterone / response to temperature stimulus / response to pain / glycogen metabolic process / response to stress / 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 / learning / kidney development / female pregnancy / negative regulation of smooth muscle cell proliferation / : / visual learning / multicellular organism growth / regulation of blood pressure / memory / response to wounding / cognition / response to estrogen / response to toxic substance / cell body / gene expression / methylation / vesicle / dendritic spine / response to oxidative stress / response to lipopolysaccharide / postsynaptic membrane / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / 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-6P2 / : / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å
AuthorsEhler, A. / Rodriguez-Sarmiento, R.M. / Rudolph, M.G.
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 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.4May 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

Downloads & links

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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)100,70322
Polymers97,9044
Non-polymers2,79918
Water10,251569
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0725
Polymers24,4761
Non-polymers5964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0725
Polymers24,4761
Non-polymers5964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2796
Polymers24,4761
Non-polymers8035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2796
Polymers24,4761
Non-polymers8035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.167, 69.963, 104.053
Angle α, β, γ (deg.)90.000, 94.180, 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: 24476.057 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 , 5 types, 587 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-6P2 / 5-{3-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-5-yl}-2,4-dimethyl-1,3-thiazole


Mass: 325.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19N3OS
#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-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.86 Å3/Da / Density % sol: 57.01 %
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: 2.02→47.26 Å / Num. obs: 72132 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.25 % / Biso Wilson estimate: 35.241 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.138 / Net I/σ(I): 6.52
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.02-2.071.2931.03197.9
2.07-2.131.0781.25198.2
2.13-2.190.8561.61197.9
2.19-2.260.6592.04198.1
2.26-2.330.532.58198
2.33-2.410.4723.21198.1
2.41-2.510.3763.85198.8
2.51-2.610.334.31198.7
2.61-2.720.2655.11199.1
2.72-2.860.2235.68199.4
2.86-3.010.1567.02199
3.01-3.190.1288.8199.4
3.19-3.410.09511.2199.3
3.41-3.690.07213.55198.5
3.69-4.040.06614.99198.6
4.04-4.520.05616.34197.4
4.52-5.220.05318.03198.3
5.22-6.390.05915.77198.5
6.39-9.030.04915.98197.8
9.030.03719.71195.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.02→45.444 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.2491 3697 5.13 %
Rwork0.1976 --
obs0.2002 72132 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.44 Å2 / Biso mean: 30.0485 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 2.02→45.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6848 0 178 569 7595
Biso mean--28.03 36.47 -
Num. residues----875

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