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- PDB-5p95: rat catechol O-methyltransferase in complex with N-[5-(6-aminopur... -

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Basic information

Entry
Database: PDB / ID: 5p95
Titlerat catechol O-methyltransferase in complex with N-[5-(6-aminopurin-9-yl)pentyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide at 1.30A
ComponentsCatechol O-methyltransferaseCatechol-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-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-77G / (4S,5S)-1,2-DITHIANE-4,5-DIOL / PHOSPHATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.B_iso_Wilson_estimate / _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_number_measured_all / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 2.2Nov 17, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_deposit_group ...database_2 / pdbx_deposit_group / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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 / _struct_conn_type.id
Revision 2.3Apr 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

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Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8089
Polymers24,7721
Non-polymers1,0368
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.994, 54.030, 80.843
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 / Catechol-O-methyltransferase


Mass: 24772.400 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-264
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, 350 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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-77G / N-[5-(6-aminopurin-9-yl)pentyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide


Mass: 450.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23FN6O3
#5: 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
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 44.19 %
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: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→40.42 Å / Num. obs: 54119 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.85 % / Biso Wilson estimate: 16.69 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.47
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.46 / % possible all: 90.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0088refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE MODEL

Resolution: 1.3→40.42 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.31 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ADENINE PART HAS TWO CONFORMATIONS THAT ARE COUPLED TO THE NEARBY TRP. OXIDIZED DTE AND CHES BUFFER ARE SUPERIMPOSED NEAR FLUOROPHENYL MOIETY. SEVERAL PARTIALLY OCCUPIED WATER MOLECULES MODELED IN BINDING SITE
RfactorNum. reflection% reflectionSelection details
Rfree0.157 2677 5.1 %RANDOM
Rwork0.121 ---
obs0.123 50171 96.6 %-
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: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 63 342 2088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221958
X-RAY DIFFRACTIONr_bond_other_d0.0020.021310
X-RAY DIFFRACTIONr_angle_refined_deg1.8432.0342686
X-RAY DIFFRACTIONr_angle_other_deg1.0333229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45825.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98415341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9241510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6771.51143
X-RAY DIFFRACTIONr_mcbond_other0.7351.5461
X-RAY DIFFRACTIONr_mcangle_it2.45721866
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5583815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8564.5803
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.65633268
X-RAY DIFFRACTIONr_sphericity_free8.9623351
X-RAY DIFFRACTIONr_sphericity_bonded3.43833210
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 177 -
Rwork0.198 3108 -
obs--81.92 %

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