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- PDB-6gy1: rat COMT in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6gy1
Titlerat COMT in complex with inhibitor
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Magnesium Ion Binding / O-Methyltransferase Activity / Neurotransmitter Catabolic Process
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-FGQ / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSchulze, M.-S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Optimization of 8-Hydroxyquinolines as Inhibitors of Catechol O-Methyltransferase.
Authors: Buchler, I. / Akuma, D. / Au, V. / Carr, G. / de Leon, P. / DePasquale, M. / Ernst, G. / Huang, Y. / Kimos, M. / Kolobova, A. / Poslusney, M. / Wei, H. / Swinnen, D. / Montel, F. / Moureau, ...Authors: Buchler, I. / Akuma, D. / Au, V. / Carr, G. / de Leon, P. / DePasquale, M. / Ernst, G. / Huang, Y. / Kimos, M. / Kolobova, A. / Poslusney, M. / Wei, H. / Swinnen, D. / Montel, F. / Moureau, F. / Jigorel, E. / Schulze, M.E.D. / Wood, M. / Barrow, J.C.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7215
Polymers24,9171
Non-polymers8044
Water75742
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.410, 50.410, 168.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase


Mass: 24916.531 Da / Num. of mol.: 1
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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Non-polymers , 5 types, 46 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-FGQ / 7-fluoranyl-5-(4-methylphenyl)sulfonyl-quinolin-8-ol


Mass: 317.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12FNO3S
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris propane, 100 mM NaCl, 1.2-1.8 M (NH4)2SO4
PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→56.111 Å / Num. all: 15123 / Num. obs: 15123 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.91 Å2 / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Rsym value: 0.073 / Net I/av σ(I): 6.6 / Net I/σ(I): 8 / Num. measured all: 51463
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.1-2.213.50.3032.521400.1890.3590.30399.5
2.21-2.353.10.2821.920010.1940.3450.28298.1
2.35-2.513.50.1465.119400.090.1720.14699.6
2.51-2.713.50.1186.317950.0720.1390.11899.7
2.71-2.973.50.0828.417010.050.0970.08299.7
2.97-3.323.50.0610.815190.0360.0710.0699.6
3.32-3.833.40.069.813570.0370.0710.0699.4
3.83-4.73.40.05210.411640.0310.0610.05299.6
4.7-6.643.40.04312.19360.0270.0510.04399.5
6.64-42.25830.0411.65700.0260.0480.0498.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S68

3s68


Resolution: 2.1→42.258 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.2489 744 4.99 %
Rwork0.2123 --
obs0.2141 14913 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.69 Å2 / Biso mean: 30.3001 Å2 / Biso min: 16.15 Å2
Refinement stepCycle: final / Resolution: 2.1→42.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 53 42 1767
Biso mean--29.69 27.77 -
Num. residues----212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.26220.33921440.30772621276593
2.2622-2.48990.29661680.23742775294399
2.4899-2.85010.3041490.23742837298699
2.8501-3.59050.27191340.22252916305099
3.5905-42.26670.18471490.17263020316999

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