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- PDB-5k0e: Crystal Structure of COMT in complex with 2,4-dimethyl-5-[3-(2-ph... -

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Basic information

Entry
Database: PDB / ID: 5k0e
TitleCrystal Structure of COMT in complex with 2,4-dimethyl-5-[3-(2-phenylpropan-2-yl)-1H-pyrazol-5-yl]-1,3-thiazole
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 / 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 / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / glomerulus development / fear response / multicellular organismal reproductive process / 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 pain / response to corticosterone / dopamine metabolic process / prostaglandin metabolic process / glycogen 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 / response to cytokine / kidney development / 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 / postsynapse / methylation / postsynaptic membrane / vesicle / 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 / O-methyltransferase / Class I-like SAM-dependent 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-6OZ / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsEhler, A. / Rodriguez-Sarmiento, R.M. / Rudolph, M.G.
CitationJournal: To Be Published
Title: Crystal Structure of COMT
Authors: Ehler, A. / Rodriguez-Sarmiento, R.M. / Rudolph, M.G.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)24,6115
Polymers24,0481
Non-polymers5634
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-17 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.793, 108.307, 69.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase


Mass: 24047.529 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

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Non-polymers , 5 types, 61 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-6OZ / 2,4-dimethyl-5-[3-(2-phenylpropan-2-yl)-1H-pyrazol-5-yl]-1,3-thiazole


Mass: 297.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
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: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.3→46.69 Å / Num. obs: 13292 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.17 % / Biso Wilson estimate: 51.121 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Net I/σ(I): 9.02
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.361.6751.37199.7
2.36-2.421.5161.48199.4
2.42-2.51.2521.87199.2
2.5-2.571.0382.16199.7
2.57-2.660.8072.72199.7
2.66-2.750.6513.2199.4
2.75-2.850.5124.11199.7
2.85-2.970.4095.34199.7
2.97-3.10.2727.28199.9
3.1-3.250.2079.22199.9
3.25-3.430.15810.99199.7
3.43-3.640.10514.21199.4
3.64-3.890.08616.83199.7
3.89-4.20.07119.29198.8
4.2-4.60.06422.11199.4
4.6-5.140.06320.99199.4
5.14-5.940.06319.81199.8
5.94-7.270.0621.7199.2
7.27-10.290.04824.59199.7
10.290.0427.03197.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.3→42.671 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.12
RfactorNum. reflection% reflection
Rfree0.2553 654 4.96 %
Rwork0.1924 --
obs0.1954 13196 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.81 Å2 / Biso mean: 54.5162 Å2 / Biso min: 21.76 Å2
Refinement stepCycle: final / Resolution: 2.3→42.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 36 57 1776
Biso mean--39.95 44.86 -
Num. residues----215
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)
16.3491-4.7594-5.82173.72364.37585.3633-0.7688-1.1630.2530.94990.6141-0.29720.51350.9218-0.00780.46320.0071-0.03530.6439-0.00880.375417.2315-35.374710.0667
29.83653.3376-2.80618.2791-5.33093.4779-0.10130.1255-0.9534-0.0214-0.0508-0.55070.68590.27140.22130.41790.0430.02740.406-0.05850.440615.2597-41.97511.7497
37.2108-1.76667.12045.5868-3.34059.66030.49280.4214-0.7341-0.0681-0.0440.21860.73331.0473-0.38140.4720.06640.09070.5321-0.04760.51041.9982-44.9412-0.7261
45.1808-0.2962-0.08631.5319-0.29251.29930.02510.4190.2869-0.076-0.043-0.08640.0346-0.03130.01080.2934-0.0492-0.00910.45630.03550.30462.0444-29.0642-0.1085
55.35950.03441.32813.2732-0.96886.1237-0.03480.35520.1702-0.07740.06910.1794-0.0671-0.0375-0.0480.2385-0.02930.0030.4495-0.05290.3211-10.5196-31.36192.3083
61.74-0.66150.15914.7052-0.39233.02150.09780.2622-0.23420.1693-0.02520.41580.3854-0.2398-0.11320.3768-0.0892-0.01440.5413-0.05830.4001-12.654-42.86171.4653
75.5212-4.68313.7225.165-5.20028.6382-0.30580.1731-0.02330.5454-0.033-0.17230.20550.02930.56160.5892-0.0767-0.14860.5046-0.17090.6294-8.8385-45.98532.6476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )A2 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 36 )A17 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 57 )A37 - 57
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 129 )A58 - 129
5X-RAY DIFFRACTION5chain 'A' and (resid 130 through 157 )A130 - 157
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 198 )A158 - 198
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 216 )A199 - 216

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