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- PDB-7xjb: Rat-COMT, opicapone,SAM and Mg bond -

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Basic information

Entry
Database: PDB / ID: 7xjb
TitleRat-COMT, opicapone,SAM and Mg bond
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Enzyme S-adenosylmethionone catechol / catecholamine
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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Opicapone / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTakebe, K. / Iijima, H. / Suzuki, M. / Kuwada-Kusunose, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP15K08034 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101001 (0318) 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 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 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
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,21022
Polymers99,6664
Non-polymers3,54418
Water3,981221
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8116
Polymers24,9171
Non-polymers8945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area9400 Å2
MethodPISA
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7885
Polymers24,9171
Non-polymers8714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area9350 Å2
MethodPISA
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7885
Polymers24,9171
Non-polymers8714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area8760 Å2
MethodPISA
4
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8236
Polymers24,9171
Non-polymers9075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.158, 166.158, 125.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 10 or (resid 11...
21(chain B and (resid 3 through 10 or (resid 11...
31(chain C and (resid 3 through 22 or resid 24...
41(chain D and (resid 3 through 17 or (resid 18...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU(chain A and (resid 3 through 10 or (resid 11...AA3 - 105 - 12
12ARGARGARGARG(chain A and (resid 3 through 10 or (resid 11...AA1113
13SERSERSERSER(chain A and (resid 3 through 10 or (resid 11...AA0 - 2162 - 218
14SERSERSERSER(chain A and (resid 3 through 10 or (resid 11...AA0 - 2162 - 218
15SERSERSERSER(chain A and (resid 3 through 10 or (resid 11...AA0 - 2162 - 218
16SERSERSERSER(chain A and (resid 3 through 10 or (resid 11...AA0 - 2162 - 218
21ASPASPLEULEU(chain B and (resid 3 through 10 or (resid 11...BB3 - 105 - 12
22ARGARGARGARG(chain B and (resid 3 through 10 or (resid 11...BB1113
23SERSERSERSER(chain B and (resid 3 through 10 or (resid 11...BB0 - 2162 - 218
24SERSERSERSER(chain B and (resid 3 through 10 or (resid 11...BB0 - 2162 - 218
25SERSERSERSER(chain B and (resid 3 through 10 or (resid 11...BB0 - 2162 - 218
26SERSERSERSER(chain B and (resid 3 through 10 or (resid 11...BB0 - 2162 - 218
31ASPASPPROPRO(chain C and (resid 3 through 22 or resid 24...CC3 - 225 - 24
32SERSERTHRTHR(chain C and (resid 3 through 22 or resid 24...CC24 - 3426 - 36
33LYSLYSLYSLYS(chain C and (resid 3 through 22 or resid 24...CC3638
34ASPASPPROPRO(chain C and (resid 3 through 22 or resid 24...CC3 - 2155 - 217
35GLUGLUGLUGLU(chain C and (resid 3 through 22 or resid 24...CC3739
41ASPASPALAALA(chain D and (resid 3 through 17 or (resid 18...DD3 - 175 - 19
42LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD1820
43PROPROPROPRO(chain D and (resid 3 through 17 or (resid 18...DD19 - 2221 - 24
44SERSERTHRTHR(chain D and (resid 3 through 17 or (resid 18...DD24 - 3426 - 36
45LYSLYSTHRTHR(chain D and (resid 3 through 17 or (resid 18...DD36 - 9938 - 101
46GLNGLNGLNGLN(chain D and (resid 3 through 17 or (resid 18...DD100102
47GLNGLNLEULEU(chain D and (resid 3 through 17 or (resid 18...DD101 - 108103 - 110
48GLNGLNGLNGLN(chain D and (resid 3 through 17 or (resid 18...DD109111
49ASPASPLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD110 - 128112 - 130
410LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD129131
411TYRTYRGLUGLU(chain D and (resid 3 through 17 or (resid 18...DD130 - 155132 - 157
412LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD156158
413CYSCYSARGARG(chain D and (resid 3 through 17 or (resid 18...DD157 - 161159 - 163
414LYSLYSLYSLYS(chain D and (resid 3 through 17 or (resid 18...DD162164
415GLYGLYPROPRO(chain D and (resid 3 through 17 or (resid 18...DD163 - 215165 - 217

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Catechol O-methyltransferase


Mass: 24916.531 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 (bacteria) / Strain (production host): BL21 / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 6 types, 239 molecules

#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#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.: 4 / Source method: obtained synthetically / Formula: C15H10Cl2N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.35 Å3/Da / Density % sol: 71.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000 Litium sulfate

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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: 2.6→12 Å / Num. obs: 54691 / % possible obs: 100 % / Redundancy: 16.8 % / CC1/2: 0.997 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.68 Å / Num. unique obs: 4433 / CC1/2: 0.774

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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: 2.6→11.996 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 2747 5.09 %
Rwork0.1624 51230 -
obs0.1641 53977 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.32 Å2 / Biso mean: 43.7435 Å2 / Biso min: 22.44 Å2
Refinement stepCycle: final / Resolution: 2.6→11.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6687 0 226 221 7134
Biso mean--41.58 42.54 -
Num. residues----860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2528X-RAY DIFFRACTION3.571TORSIONAL
12B2528X-RAY DIFFRACTION3.571TORSIONAL
13C2528X-RAY DIFFRACTION3.571TORSIONAL
14D2528X-RAY DIFFRACTION3.571TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6-2.64440.29751330.2352519
2.6444-2.69190.26051280.21622553
2.6919-2.74310.23231470.21762506
2.7431-2.79840.21941340.20992533
2.7984-2.85840.26161350.2122527
2.8584-2.9240.25691260.20312535
2.924-2.9960.23031460.18682526
2.996-3.07570.24771330.18912540
3.0757-3.16460.20531410.18412527
3.1646-3.26480.22141300.17162555
3.2648-3.37890.20861230.17112559
3.3789-3.5110.17061390.15372557
3.511-3.66640.1911550.14732534
3.6664-3.85360.19321320.14622562
3.8536-4.08610.18251160.1392603
4.0861-4.38720.14211530.13212551
4.3872-4.80280.14981310.12382594
4.8028-5.44020.17071410.1452611
5.4402-6.65350.20071390.18052651
6.6535-11.9960.18851650.15332687
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6982-0.06630.81431.4424-0.6061.7352-0.0187-0.10740.09130.064-0.0530.0053-0.04850.03030.07330.2339-0.00120.03250.2019-0.02330.1915-75.867316.736637.8311
21.03770.04210.4372.0004-0.96771.5186-0.02980.04870.0089-0.1002-0.0309-0.04080.02130.05440.05850.21080.02120.01820.2511-0.02650.2027-65.12583.46212.534
32.39860.3977-0.61641.64580.27371.9088-0.01240.01210.3007-0.06520.02890.0031-0.29690.1367-0.01290.3614-0.0355-0.05950.26660.02230.3391-67.866546.159224.2591
41.87210.52140.21362.82890.71272.19030.04920.1149-0.0608-0.10710.0496-0.4779-0.06270.5119-0.0940.249-0.00030.01940.42880.05010.3454-34.64354.968426.4604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 216)A0 - 216
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 216)B0 - 216
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 215)C3 - 215
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 215)D3 - 215

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