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- PDB-5p9z: humanized rat COMT in complex with 6-(4-fluorophenyl)quinazolin-8-ol -

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Basic information

Entry
Database: PDB / ID: 5p9z
Titlehumanized rat COMT in complex with 6-(4-fluorophenyl)quinazolin-8-ol
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION
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
6-(4-fluorophenyl)quinazolin-8-ol / (4S,5S)-1,2-DITHIANE-4,5-DIOL / S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a COMT complex
Authors: Lerner, C. / Jakob-Roetne, R. / Groebke-Zbinden, K. / Buettelmann, B. / Rudolph, M.G.
History
DepositionOct 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 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_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_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.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)25,6628
Polymers24,6941
Non-polymers9687
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.094, 54.411, 80.853
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 / Humanized rat COMT


Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264 / Mutation: M134I, Y138C
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 , 7 types, 213 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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#6: Chemical ChemComp-7JQ / 6-(4-fluorophenyl)quinazolin-8-ol


Mass: 240.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9FN2O
#7: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→27.21 Å / Num. obs: 28335 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 6.32 % / Biso Wilson estimate: 19.652 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.058 / Χ2: 0.973 / Net I/σ(I): 21.64 / Num. measured all: 179052
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.640.2096.9715757217921790.9830.225100
1.64-1.690.1887.8515332212221210.9850.202100
1.69-1.740.2468.7412272205019460.970.26994.9
1.74-1.790.14910.214377200619870.9910.1699.1
1.79-1.850.12512.3114035194519360.9930.13499.5
1.85-1.910.14513.426936187714960.9880.16679.7
1.91-1.980.10216.597497182816010.9920.11787.6
1.98-2.070.08818.458820176815580.9920.09988.1
2.07-2.160.07221.68530168315250.9940.08290.6
2.16-2.260.0722.777501162214640.9880.0890.3
2.26-2.390.05426.919460155714740.9860.0694.7
2.39-2.530.04131.1310555144714420.9990.04499.7
2.53-2.70.05329.947532138313280.9950.05996
2.7-2.920.03935.818876127912590.9990.04298.4
2.92-3.20.03140.78739120812080.9990.033100
3.2-3.580.04140.166063108510450.9970.04696.3
3.58-4.130.04139.2847249769370.9960.04696
4.13-5.060.02346.56569782882710.02599.9
5.06-7.160.02344.05450366366210.02599.8
7.16-27.210.02240.3618464073400.9990.02483.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.6→27.21 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.881 / SU B: 1.958 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: amide bond kinked away from ligand, interacting with lys51. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1335 4.9 %RANDOM
Rwork0.2034 ---
obs0.2053 25834 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.32 Å2 / Biso mean: 14.583 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.57 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.6→27.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 60 206 1939
Biso mean--14.84 25.8 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021837
X-RAY DIFFRACTIONr_bond_other_d0.0020.021762
X-RAY DIFFRACTIONr_angle_refined_deg1.9012.0182509
X-RAY DIFFRACTIONr_angle_other_deg1.06234076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2775236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1524.61578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8961511
X-RAY DIFFRACTIONr_chiral_restr0.1190.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212055
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02398
X-RAY DIFFRACTIONr_mcbond_it1.3891.26881
X-RAY DIFFRACTIONr_mcbond_other1.3891.26880
X-RAY DIFFRACTIONr_mcangle_it2.141.8851105
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 100 -
Rwork0.147 1968 -
all-2068 -
obs--95.26 %

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