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- PDB-3a7d: Crystal Structures of rat Catechol-O-Methyltransferase complexed ... -

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Basic information

Entry
Database: PDB / ID: 3a7d
TitleCrystal Structures of rat Catechol-O-Methyltransferase complexed with new bi-substrate type inhibitor
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Methyltransferase / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / S-ADENOSYL-L-METHIONINE / Cell membrane / Magnesium / Membrane / Metal-binding / Phosphoprotein / 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 / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity ...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 / catechol-containing compound metabolic process / catecholamine catabolic process / catechol O-methyltransferase activity / renal sodium excretion / : / : / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / renal filtration / developmental process / renin secretion into blood stream / dopamine secretion / negative regulation of dopamine metabolic process / renal albumin absorption / catecholamine metabolic process / habituation / artery development / response to salt / short-term memory / S-adenosylmethionine metabolic process / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / cellular response to phosphate starvation / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / response to food / cholesterol efflux / response to temperature stimulus / response to pain / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / dopamine metabolic process / startle response / 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 / response to toxic substance / memory / cognition / regulation of blood pressure / response to wounding / response to estrogen / gene expression / cell body / postsynapse / methylation / postsynaptic membrane / vesicle / 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 / 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-FBN / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTsuji, E.
CitationJournal: To be Published
Title: Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 2: Ligand Fishing using Mass Spectrometry by Detection of Ligand-Protein Non-Covalent Complex after Matrix Click Chemistry
Authors: Muranaka, H. / Nakatsu, M. / Tsuji, E. / Okazaki, K.
History
DepositionSep 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6615
Polymers24,9171
Non-polymers7454
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.075, 58.082, 79.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Catechol O-methyltransferase


Mass: 24916.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FBN / 5'-deoxy-5'-[4-({[(2,3-dihydroxy-5-nitrophenyl)carbonyl]amino}methyl)-1H-1,2,3-triazol-1-yl]adenosine / N-[(1-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]-2,3-dihy droxy-5-nitrobenzamide


Mass: 528.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N10O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON ISOFORM 2 OF P22734(COMT_RAT).

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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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M (NH4)2SO4, 0.1M Tris pH 7.5, 30% (w/v) PEG 400, 0.35% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 16, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.8 Å / Num. all: 9108 / Num. obs: 9468 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.078 / Net I/σ(I): 27.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 9.1 / Num. unique all: 1282 / Rsym value: 0.236 / % possible all: 96.1

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Processing

Software
NameVersionClassification
BSSat BL32B2data collection
AMoREphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VID

1vid


Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.573 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22466 891 9.9 %RANDOM
Rwork0.1592 ---
obs0.16601 8064 96.18 %-
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 mean: 33.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--1.23 Å20 Å2
3----0.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.269 Å0.606 Å
Luzzati d res low-6 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 49 93 1818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221757
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.0182387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.875213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4424.875
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.646159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211313
X-RAY DIFFRACTIONr_mcbond_it0.9541.51062
X-RAY DIFFRACTIONr_mcangle_it1.82821708
X-RAY DIFFRACTIONr_scbond_it3.2973695
X-RAY DIFFRACTIONr_scangle_it5.1914.5679
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 62 -
Rwork0.215 533 -
obs--94.75 %

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