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- PDB-5p91: humanized rat catechol O-methyltransferase in complex with 5-(4-f... -

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Basic information

Entry
Database: PDB / ID: 5p91
Titlehumanized rat catechol O-methyltransferase in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[2-[5-(2-methylpyridin-4-yl)-4H-1,2,4-triazol-3-yl]ethyl]benzamide at 1.20A
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE/TRANSFERASE inhibitor / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex
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-containing compound metabolic process / 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-containing compound metabolic process / S-adenosylhomocysteine metabolic process / response to salt / catechol O-methyltransferase activity / renal sodium excretion / : / : / renin secretion into blood stream / developmental process / catechol O-methyltransferase / renal filtration / renal albumin absorption / dopamine secretion / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / habituation / artery development / catecholamine metabolic process / short-term memory / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / cholesterol efflux / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / response to pain / response to temperature stimulus / dopamine metabolic process / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / response to inorganic substance / behavioral fear response / multicellular organismal response to stress / response to amphetamine / learning / kidney development / response to organic substance / response to cytokine / female pregnancy / negative regulation of smooth muscle cell proliferation / multicellular organism growth / visual learning / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / cell body / gene expression / methylation / postsynaptic membrane / postsynapse / response to oxidative stress / vesicle / response to lipopolysaccharide / dendritic spine / response to hypoxia / learning or memory / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / 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-76B / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a COMT complex
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.2Nov 17, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_deposit_group ...database_2 / pdbx_deposit_group / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,5267
Polymers24,6941
Non-polymers8326
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.964, 53.762, 80.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Catechol-O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM (UNP RESIDUES 44-264) / Mutation: M91I, Y95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / 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, 235 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-76B / 5-(4-fluorophenyl)-2,3-dihydroxy-N-[2-[5-(2-methylpyridin-4-yl)-4H-1,2,4-triazol-3-yl]ethyl]benzamide / 4'-fluoro-4,5-dihydroxy-N-{2-[3-(2-methylpyridin-4-yl)-1H-1,2,4-triazol-5-yl]ethyl}[1,1'-biphenyl]-3-carboxamide


Mass: 433.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20FN5O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.2→24.98 Å / Num. obs: 68175 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.99 % / Biso Wilson estimate: 14.115 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.057 / Χ2: 0.974 / Net I/σ(I): 17.58 / Num. measured all: 339863
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.230.314.7219038498949150.9110.35998.5
1.23-1.260.2436.5324924492049170.9610.27199.9
1.26-1.30.2197.3823373477047540.9660.24699.7
1.3-1.340.1788.4623462462546050.9780.19999.6
1.34-1.390.1479.8323292452445220.9840.164100
1.39-1.430.12811.1722395433543330.9870.142100
1.43-1.490.11912.7121071419241810.9890.13399.7
1.49-1.550.08715.4521043406340550.9930.09799.8
1.55-1.620.07117.9820334389738940.9950.07999.9
1.62-1.70.06220.619493372637230.9960.06999.9
1.7-1.790.05522.6618770357635720.9970.06299.9
1.79-1.90.05224.9117190334233280.9970.05899.6
1.9-2.030.05126.6914834319431260.9960.05797.9
2.03-2.190.04330.2715170295329400.9970.04899.6
2.19-2.40.04430.9912929274026820.9970.04997.9
2.4-2.680.03933.3812895249924920.9970.04499.7
2.68-3.10.03634.7211291220821970.9980.0499.5
3.1-3.790.03635.059070190718600.9980.0497.5
3.79-5.370.03434.036190150113650.9980.03890.9
5.37-24.980.03332.6230998927140.9980.03880

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0041refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.2→24.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.966 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1612 3268 5.1 %RANDOM
Rwork0.1369 ---
obs0.1381 61386 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 41.76 Å2 / Biso mean: 9.981 Å2 / Biso min: 4.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.2→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 85 230 1988
Biso mean--14.9 21.33 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221949
X-RAY DIFFRACTIONr_bond_other_d0.0010.021298
X-RAY DIFFRACTIONr_angle_refined_deg1.7272.0312680
X-RAY DIFFRACTIONr_angle_other_deg0.93233209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1715259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6324.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31515351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4651513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212185
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
X-RAY DIFFRACTIONr_mcbond_it0.1040.212280
X-RAY DIFFRACTIONr_mcbond_other0.0830.222746
X-RAY DIFFRACTIONr_rigid_bond_restr14.765335026
X-RAY DIFFRACTIONr_sphericity_free8.7455233
X-RAY DIFFRACTIONr_sphericity_bonded4.63753185
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 219 -
Rwork0.185 4097 -
all-4316 -
obs--86.74 %

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