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- PDB-4pyq: Humanized rat apo-COMT in complex with a ureido-benzamidine -

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Basic information

Entry
Database: PDB / ID: 4pyq
TitleHumanized rat apo-COMT in complex with a ureido-benzamidine
ComponentsCatechol O-methyltransferase
KeywordsTransferase/transferase inhibitor / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MAGNESIUM / MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE / 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 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 / fear response / 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 / 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 / glycogen metabolic process / response to pain / 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 / response to cytokine / kidney development / learning / female pregnancy / negative regulation of smooth muscle cell proliferation / visual learning / multicellular organism growth / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynaptic membrane / vesicle / postsynapse / methylation / response to oxidative stress / 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-2X1 / ACETATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsEhler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Mapping the conformational space accessible to catechol-O-methyltransferase.
Authors: Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Feb 28, 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_ref_seq_dif / 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,53913
Polymers49,3892
Non-polymers1,15011
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-104 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.366, 125.366, 77.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 2 / Fragment: unp 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) / References: UniProt: P22734, catechol O-methyltransferase

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Non-polymers , 6 types, 218 molecules

#2: Chemical ChemComp-2X1 / 4-({[3-(aminomethyl)phenyl]carbamoyl}amino)benzenecarboximidamide


Mass: 283.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.37 Å3/Da / Density % sol: 48.03 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.5
ReflectionResolution: 1.39→36.4 Å / Num. obs: 91065 / % possible obs: 99.7 %
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 1.491 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1589)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→36.41 Å / σ(F): 1.96 / Phase error: 17.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.161 4574 5.02 %
Rwork0.132 --
obs0.143 91056 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 73 207 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143521
X-RAY DIFFRACTIONf_angle_d1.3334782
X-RAY DIFFRACTIONf_dihedral_angle_d15.3451335
X-RAY DIFFRACTIONf_chiral_restr0.068533
X-RAY DIFFRACTIONf_plane_restr0.006613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3892-1.41310.35922200.34364288X-RAY DIFFRACTION94
1.4131-1.43880.33012120.31184324X-RAY DIFFRACTION95
1.4388-1.46650.28632310.26554320X-RAY DIFFRACTION95
1.4665-1.49640.29281980.25074386X-RAY DIFFRACTION96
1.4964-1.5290.2532460.21814364X-RAY DIFFRACTION95
1.529-1.56460.20532220.21094333X-RAY DIFFRACTION95
1.5646-1.60370.23572430.20124304X-RAY DIFFRACTION95
1.6037-1.6470.21272490.19084339X-RAY DIFFRACTION95
1.647-1.69550.20612300.18484334X-RAY DIFFRACTION95
1.6955-1.75020.19642380.17684326X-RAY DIFFRACTION95
1.7502-1.81280.18242610.1724287X-RAY DIFFRACTION94
1.8128-1.88540.18072240.16754330X-RAY DIFFRACTION95
1.8854-1.97120.18072180.16764350X-RAY DIFFRACTION95
1.9712-2.07510.20062330.16024327X-RAY DIFFRACTION95
2.0751-2.20510.18412310.15364277X-RAY DIFFRACTION94
2.2051-2.37530.17392140.14054322X-RAY DIFFRACTION95
2.3753-2.61430.16032180.13364306X-RAY DIFFRACTION94
2.6143-2.99240.162020.12244349X-RAY DIFFRACTION95
2.9924-3.76950.1362300.10014285X-RAY DIFFRACTION94
3.7695-36.41860.12972400.09274338X-RAY DIFFRACTION95

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