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- PDB-7xgi: COMT SAH Mg opicapone complex -

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Basic information

Entry
Database: PDB / ID: 7xgi
TitleCOMT SAH Mg opicapone complex
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / enzyme / complex / S -adenosylhomocystein / Parkinson disease
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 / : / 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 / gene expression / cell body / postsynaptic membrane / methylation / vesicle / response to oxidative stress / postsynapse / 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 / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Opicapone / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTakebe, K. / Kuwada-Kusunose, T. / Suzuki, M. / Iijima, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101001 (0318) Japan
Japan Society for the Promotion of Science (JSPS)JP15K08034 Japan
CitationJournal: J.Chem.Inf.Model. / Year: 2023
Title: Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O -Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses.
Authors: Takebe, K. / Suzuki, M. / Kuwada-Kusunose, T. / Shirai, S. / Fukuzawa, K. / Takamiya, T. / Uzawa, N. / Iijima, H.
History
DepositionApr 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Structure summary / Category: audit_author
Revision 1.2Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 27, 2023Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.4Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)25,7384
Polymers24,9171
Non-polymers8223
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.756, 50.756, 168.241
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#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 BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase
#2: 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
#3: Chemical ChemComp-DNI / Opicapone / 5-[3-[2,5-bis(chloranyl)-4,6-dimethyl-1-oxidanidyl-pyridin-1-ium-3-yl]-1,2,4-oxadiazol-5-yl]-3-nitro-benzene-1,2-diol


Mass: 413.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10Cl2N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1,4-Dioxane, ammonium sulfate, MES Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→11.913 Å / Num. obs: 17598 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1259 / CC1/2: 0.968

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LFE

6lfe


Resolution: 2→11.913 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 853 4.87 %
Rwork0.1838 16669 -
obs0.1852 17522 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.65 Å2 / Biso mean: 35.9696 Å2 / Biso min: 20.06 Å2
Refinement stepCycle: final / Resolution: 2→11.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 54 83 1810
Biso mean--42.55 40.45 -
Num. residues----213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.12470.29941790.2197266299
2.1247-2.28770.24171240.2051273698
2.2877-2.51590.25171530.1996271499
2.5159-2.87550.20671530.1983274199
2.8755-3.60610.2004960.1885286399
3.6061-11.9130.19791480.1626295399
Refinement TLS params.Method: refined / Origin x: 27.0157 Å / Origin y: -5.3697 Å / Origin z: -12.0842 Å
111213212223313233
T0.2443 Å2-0.1074 Å20.0026 Å2-0.2993 Å2-0.0102 Å2--0.2064 Å2
L1.3189 °2-0.1043 °2-0.2537 °2-2.4251 °20.8308 °2--3.374 °2
S-0.0566 Å °0.2387 Å °-0.0233 Å °-0.1341 Å °0.1105 Å °-0.0405 Å °-0.0586 Å °0.2066 Å °-0.0627 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 3 through 215)

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