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- PDB-5k03: Crystal Structure of COMT in complex with 2,6-dimethyl-3-(1H-pyra... -

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Basic information

Entry
Database: PDB / ID: 5k03
TitleCrystal Structure of COMT in complex with 2,6-dimethyl-3-(1H-pyrazol-3-yl)imidazo[1,2-a]pyridine
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 / renal sodium excretion / developmental process / 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 / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / exploration behavior / response to stress / multicellular organismal response to stress / behavioral fear response / 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 / response to estrogen / regulation of blood pressure / cognition / multicellular organism growth / memory / cell body / response to oxidative stress / response to lipopolysaccharide / methylation / vesicle / gene expression / 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-6P4 / : / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2423
Polymers23,9911
Non-polymers2512
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint0 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.357, 59.670, 106.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catechol O-methyltransferase


Mass: 23990.541 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-6P4 / 2,6-dimethyl-3-(1H-pyrazol-5-yl)imidazo[1,2-a]pyridine


Mass: 212.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
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: Mar 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.71 Å / Num. obs: 19947 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 34.292 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.851.4721.06198.5
1.85-1.91.7851.06198.2
1.9-1.950.8652197.2
1.95-2.010.7332.3198.2
2.01-2.080.6062.85198.1
2.08-2.150.4863.64197.9
2.15-2.230.4414.35197
2.23-2.320.3455.61197.2
2.32-2.430.276.89198.1
2.43-2.550.228.11198.2
2.55-2.680.1928.99198.6
2.68-2.850.15110.58197.7
2.85-3.040.11512.8197.3
3.04-3.290.08215.8198.3
3.29-3.60.06918.21196
3.6-4.020.06418.44195.6
4.02-4.650.05220.66195.4
4.65-5.690.05221.09193.8
5.69-8.050.0520.08194.6
8.05-39.710.03822.08191.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.81→30.487 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.91
RfactorNum. reflection% reflection
Rfree0.253 1001 5.07 %
Rwork0.1985 --
obs0.2013 19728 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.93 Å2 / Biso mean: 27.962 Å2 / Biso min: 8.48 Å2
Refinement stepCycle: final / Resolution: 1.81→30.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 17 185 1881
Biso mean--20.56 38.3 -
Num. residues----214
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)
10.8140.346-0.77120.5479-0.38851.0812-0.2557-0.0236-0.1806-0.2077-0.0404-0.09880.28760.052-0.380.23370.03710.00050.16960.00750.12578.00043.07892.9823
20.12690.0034-0.0010.1467-0.15580.1590.1156-0.24270.1673-0.0983-0.0207-0.2130.19330.0750.0040.20840.0360.01520.30660.03370.22212.70836.310716.9934
30.23370.2130.240.33030.41520.6544-0.02430.05390.0606-0.13480.01070.0167-0.11040.016700.13390.0272-0.00770.132-0.00770.10859.29719.47713.1322
40.34030.1596-0.08360.14770.04950.10690.0677-0.1675-0.05460.1812-0.0756-0.05680.0002-0.0344-0.00030.16090.0082-0.00440.1422-0.0130.1489.095915.300229.7999
50.1254-0.07680.09940.0512-0.0410.0814-0.0564-0.1595-0.07090.13110.1569-0.22560.03480.09140.00010.1515-0.02110.01020.1696-0.01150.15086.41148.023127.6363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 35 )A3 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 57 )A36 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 143 )A58 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 198 )A144 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 216 )A199 - 216

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