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- PDB-4p58: Crystal structure of mouse comt bound to an inhibitor -

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Basic information

Entry
Database: PDB / ID: 4p58
TitleCrystal structure of mouse comt bound to an inhibitor
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / SAM binding site / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / positive regulation of homocysteine metabolic process / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / positive regulation of homocysteine metabolic process / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / 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 / 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 / prostaglandin metabolic process / 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 / response to cytokine / kidney development / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to toxic substance / memory / cognition / regulation of blood pressure / response to wounding / gene expression / cell body / postsynapse / methylation / postsynaptic membrane / vesicle / response to oxidative stress / dendritic spine / learning or memory / response to hypoxia / response to xenobiotic stimulus / axon / intracellular membrane-bounded organelle / glutamatergic synapse / dendrite / magnesium ion binding / mitochondrion / 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
1',3'-dimethyl-1H,1'H-3,4'-bipyrazole / Catechol O-methyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsLanier, M.
CitationJournal: J.Med.Chem. / Year: 2014
Title: A fragment-based approach to identifying S-adenosyl-l-methionine -competitive inhibitors of catechol O-methyl transferase (COMT).
Authors: Lanier, M. / Ambrus, G. / Cole, D.C. / Davenport, R. / Ellery, J. / Fosbeary, R. / Jennings, A.J. / Kadotani, A. / Kamada, Y. / Kamran, R. / Matsumoto, S. / Mizukami, A. / Okubo, S. / Okada, ...Authors: Lanier, M. / Ambrus, G. / Cole, D.C. / Davenport, R. / Ellery, J. / Fosbeary, R. / Jennings, A.J. / Kadotani, A. / Kamada, Y. / Kamran, R. / Matsumoto, S. / Mizukami, A. / Okubo, S. / Okada, K. / Saikatendu, K. / Walsh, L. / Wu, H. / Hixon, M.S.
History
DepositionMar 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9972
Polymers23,8341
Non-polymers1621
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.584, 98.584, 115.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Catechol O-methyltransferase


Mass: 23834.354 Da / Num. of mol.: 1 / Fragment: UNP residues 47-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Comt, Comt1 / Production host: Escherichia coli (E. coli) / References: UniProt: O88587, catechol O-methyltransferase
#2: Chemical ChemComp-2F6 / 1',3'-dimethyl-1H,1'H-3,4'-bipyrazole


Mass: 162.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M NaCl and 0.1 M Na-acetate pH 4.6 at 4C, drop ratio 100nl + 100nl
PH range: 4.5-4.9

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryo stream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 17238 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Redundancy: 4.7 % / Net I/σ(I): 22.65
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 4.7 % / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NW9

3nw9


Resolution: 2.06→41.17 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.727 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 632 3.5 %RANDOM
Rwork0.145 17238 --
obs0.1472 17870 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.31 Å2 / Biso mean: 29.179 Å2 / Biso min: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0 Å20 Å2
2---0.7 Å2-0 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 2.06→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 12 150 1772
Biso mean--25.75 55.31 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021666
X-RAY DIFFRACTIONr_bond_other_d0.0010.021603
X-RAY DIFFRACTIONr_angle_refined_deg1.1912.0032260
X-RAY DIFFRACTIONr_angle_other_deg0.7433699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7465207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53824.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66515296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.544159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_mcbond_it2.5412.56822
X-RAY DIFFRACTIONr_mcbond_other2.5332.558821
X-RAY DIFFRACTIONr_mcangle_it3.2623.8261025
X-RAY DIFFRACTIONr_rigid_bond_restr2.40233266
X-RAY DIFFRACTIONr_sphericity_free38.03581
X-RAY DIFFRACTIONr_sphericity_bonded9.35953306
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.213 1290 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 9.96 Å / Origin y: 11.955 Å / Origin z: 22.535 Å
111213212223313233
T0.1073 Å2-0.0436 Å20.0013 Å2-0.0519 Å20.0025 Å2--0.0062 Å2
L1.7867 °20.1877 °2-0.281 °2-1.9683 °20.9534 °2--2.0875 °2
S-0.0041 Å °-0.1407 Å °0.0304 Å °-0.0259 Å °-0.0343 Å °0.0792 Å °-0.013 Å °-0.0682 Å °0.0384 Å °

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