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- PDB-3hvh: Rat catechol O-methyltransferase in complex with a catechol-type,... -

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Basic information

Entry
Database: PDB / ID: 3hvh
TitleRat catechol O-methyltransferase in complex with a catechol-type, N6-methyladenine-containing bisubstrate inhibitor
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / Alternative initiation / Catecholamine metabolism / Cell membrane / Magnesium / Membrane / Metal-binding / Phosphoprotein / S-adenosyl-L-methionine / Signal-anchor / Transmembrane
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 / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...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 / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / dopamine secretion / renin secretion into blood stream / negative regulation of dopamine metabolic process / catecholamine metabolic process / renal albumin absorption / artery development / habituation / short-term memory / cerebellar cortex morphogenesis / S-adenosylmethionine metabolic process / response to salt / dopamine catabolic process / cellular response to phosphate starvation / glomerulus development / norepinephrine metabolic process / fear response / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / response to stress / response to food / exploration behavior / response to temperature stimulus / response to corticosterone / prostaglandin metabolic process / response to pain / glycogen metabolic process / 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 / 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 / memory / regulation of blood pressure / response to wounding / cognition / response to toxic substance / response to estrogen / gene expression / cell body / postsynaptic membrane / vesicle / methylation / response to oxidative stress / postsynapse / 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 / 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-542 / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEhler, A. / Schlatter, D. / Stihle, M. / Benz, J. / Rudolph, M.G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Molecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor.
Authors: Ellermann, M. / Jakob-Roetne, R. / Lerner, C. / Borroni, E. / Schlatter, D. / Roth, D. / Ehler, A. / Rudolph, M.G. / Diederich, F.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2012Group: Database references / Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)26,07410
Polymers24,7721
Non-polymers1,3029
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.587, 56.248, 78.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catechol O-methyltransferase


Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, UNP RESIDUES 44-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: LIVER / Plasmid: pDS56/RBSII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 6 types, 295 molecules

#2: Chemical ChemComp-542 / N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-methylaminopurin-9-yl)oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide


Mass: 536.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25FN6O6
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→31.02 Å / Num. obs: 54871 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 18.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1007 / Rsym value: 0.523 / % possible all: 68.6

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Processing

Software
NameVersionClassification
COMOphasing
REFMAC5.5.0088refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.02 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.296 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15293 2579 5 %RANDOM
Rwork0.12954 ---
obs0.13073 48922 91.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 81 286 2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221905
X-RAY DIFFRACTIONr_bond_other_d0.0010.021288
X-RAY DIFFRACTIONr_angle_refined_deg1.7562.0272612
X-RAY DIFFRACTIONr_angle_other_deg0.99533182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80924.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42115340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7581511
X-RAY DIFFRACTIONr_chiral_restr0.1160.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212083
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
X-RAY DIFFRACTIONr_mcbond_it1.8381.51116
X-RAY DIFFRACTIONr_mcbond_other0.8811.5449
X-RAY DIFFRACTIONr_mcangle_it2.68221824
X-RAY DIFFRACTIONr_scbond_it3.7573789
X-RAY DIFFRACTIONr_scangle_it5.3454.5771
X-RAY DIFFRACTIONr_rigid_bond_restr1.75733193
X-RAY DIFFRACTIONr_sphericity_free9.8273292
X-RAY DIFFRACTIONr_sphericity_bonded4.38133139
LS refinement shellResolution: 1.298→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 126 -
Rwork0.193 2557 -
obs--65.26 %

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