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- PDB-5k05: Crystal Structure of COMT in complex with 4-methyl-2-(4-methylphe... -

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Basic information

Entry
Database: PDB / ID: 5k05
TitleCrystal Structure of COMT in complex with 4-methyl-2-(4-methylphenyl)-5-(1H-pyrazol-5-yl)-1,3-thiazole
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / CATECHOL
Function / homology
Function and homology information


: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process ...: / response to olanzapine / response to risperidone / 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 / S-adenosylmethionine metabolic process / renin secretion into blood stream / catecholamine metabolic process / dopamine secretion / renal albumin absorption / habituation / artery development / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / response to angiotensin / fear response / short-term memory / synaptic transmission, dopaminergic / cellular response to phosphate starvation / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / prostaglandin metabolic process / response to pain / response to food / response to corticosterone / response to temperature stimulus / glycogen metabolic process / negative regulation of dopamine metabolic process / response to stress / startle response / exploration behavior / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to cytokine / response to amphetamine / learning / kidney development / negative regulation of smooth muscle cell proliferation / female pregnancy / visual learning / response to wounding / response to toxic substance / regulation of blood pressure / response to estrogen / cognition / multicellular organism growth / memory / cell body / response to oxidative stress / response to lipopolysaccharide / methylation / gene expression / vesicle / dendritic spine / 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-6P5 / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 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 / 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
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16411
Polymers47,9812
Non-polymers1,1839
Water3,081171
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5345
Polymers23,9901
Non-polymers5444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6306
Polymers23,9901
Non-polymers6405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.680, 64.680, 220.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Catechol O-methyltransferase


Mass: 23990.475 Da / Num. of mol.: 2
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-6P5 / 4-methyl-2-(4-methylphenyl)-5-(1H-pyrazol-5-yl)-1,3-thiazole


Mass: 255.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13N3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.59 Å / Num. obs: 32353 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.52 % / Biso Wilson estimate: 49.707 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Net I/σ(I): 9.09
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.152.6440.79199.8
2.15-2.212.2570.99199.6
2.21-2.281.9241.23199.4
2.28-2.351.3131.78199.9
2.35-2.431.0092.33199.8
2.43-2.510.8122.85199.8
2.51-2.60.6543.6199.9
2.6-2.710.5134.66199.8
2.71-2.830.3826.25199.9
2.83-2.970.2838.3199.9
2.97-3.130.21310.631100
3.13-3.320.1514.01199.9
3.32-3.550.11717.511100
3.55-3.830.10719.34199.9
3.83-4.20.08622.411100
4.2-4.70.07224.33199.9
4.7-5.420.07723.881100
5.42-6.640.07323.71199.9
6.64-9.390.05126.41199.6
9.390.03929.94198

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.14→39.335 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2351 1536 5.04 %
Rwork0.1794 --
obs0.1821 30454 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.78 Å2 / Biso mean: 49.1383 Å2 / Biso min: 23.5 Å2
Refinement stepCycle: final / Resolution: 2.14→39.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 71 171 3594
Biso mean--70.76 49.18 -
Num. residues----427
Refinement TLS params.Method: refined / Origin x: 12.2307 Å / Origin y: 26.9589 Å / Origin z: -18.6145 Å
111213212223313233
T0.3151 Å20.0002 Å20.0174 Å2-0.2255 Å20.0017 Å2--0.2528 Å2
L0.5103 °2-0.3592 °2-0.0184 °2-0.7688 °20.0956 °2--0.6439 °2
S0.0213 Å °-0.0123 Å °-0.0084 Å °-0.1165 Å °0.0008 Å °0.0218 Å °0.0638 Å °0.0222 Å °-0.0245 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 216
2X-RAY DIFFRACTION1allB3 - 215
3X-RAY DIFFRACTION1allC2
4X-RAY DIFFRACTION1allC3
5X-RAY DIFFRACTION1allE1 - 7
6X-RAY DIFFRACTION1allS1 - 158
7X-RAY DIFFRACTION1allS159 - 163
8X-RAY DIFFRACTION1allS164 - 170
9X-RAY DIFFRACTION1allS171 - 172

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