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- PDB-2cl5: Catechol-O-methyltransferase in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 2cl5
TitleCatechol-O-methyltransferase in complex with an inhibitor
ComponentsCATECHOL O-METHYLTRANSFERASE
KeywordsTRANSFERASE / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / NEUROTRANSMITTER DEGRADATION / CATECHOL-O-METHYLTRANSFERASE / PHOSPHORYLATION / METHYLTRANSFERASE / SIGNAL-ANCHOR / TRANSMEMBRANE / COMT INHIBITOR / MEMBRANE / MAGNESIUM / METAL-BINDING
Function / homology
Function and homology information


positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / 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 / S-adenosylmethionine metabolic process / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / artery development / habituation / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / short-term memory / fear response / response to angiotensin / synaptic transmission, dopaminergic / cellular response to phosphate starvation / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / prostaglandin metabolic process / response to food / response to pain / negative regulation of dopamine metabolic process / response to corticosterone / response to temperature stimulus / glycogen metabolic process / response to stress / : / startle response / exploration behavior / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to cytokine / response to amphetamine / female pregnancy / learning / negative regulation of smooth muscle cell proliferation / kidney development / visual learning / regulation of blood pressure / response to toxic substance / response to wounding / multicellular organism growth / response to estrogen / cognition / memory / cell body / response to lipopolysaccharide / methylation / vesicle / dendritic spine / response to oxidative stress / gene expression / postsynaptic membrane / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / 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
(3,4-DIHYDROXY-2-NITROPHENYL)(PHENYL)METHANONE / (R,R)-2,3-BUTANEDIOL / S-ADENOSYLMETHIONINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPalma, P.N. / Rodrigues, M.L. / Archer, M. / Bonifacio, M.J. / Loureiro, A.I. / Learmonth, D.A. / Carrondo, M.A. / Soares-Da-Silva, P.
Citation
Journal: Mol.Pharmacol. / Year: 2006
Title: Comparative Study of Ortho- and Meta-Nitrated Inhibitors of Catechol-O-Methyltransferase: Interactions with the Active Site and Regioselectivity of O-Methylation.
Authors: Palma, P.N. / Rodrigues, M.L. / Archer, M. / Bonifacio, M.J. / Loureiro, A.I. / Learmonth, D.A. / Carrondo, M.A. / Soares-Da-Silva, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Catechol-O-Methyltransferase-Inhibitor Complex
Authors: Rodrigues, M.L. / Bonifacio, M.J. / Soares-Da-Silva, P. / Carrondo, M.A. / Archer, M.
History
DepositionApr 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATECHOL O-METHYLTRANSFERASE
B: CATECHOL O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,37412
Polymers49,5452
Non-polymers1,83010
Water9,980554
1
A: CATECHOL O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6356
Polymers24,7721
Non-polymers8625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CATECHOL O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7406
Polymers24,7721
Non-polymers9675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.767, 79.627, 61.540
Angle α, β, γ (deg.)90.00, 91.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CATECHOL O-METHYLTRANSFERASE


Mass: 24772.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: QIAGEN MIDI / 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, 564 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-BIE / (3,4-DIHYDROXY-2-NITROPHENYL)(PHENYL)METHANONE / BIA 3-335


Mass: 259.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9NO5
#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 6.5 / Details: 8% PEG6K, 0.1 M MES PH 6.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→24.42 Å / Num. obs: 67299 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.6
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1D

1h1d


Resolution: 1.6→62.02 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.37 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3396 5.1 %RANDOM
Rwork0.149 ---
obs0.151 63648 100 %-
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: 15.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-0.54 Å2
2---1.06 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.6→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 124 554 4047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223616
X-RAY DIFFRACTIONr_bond_other_d0.0020.023276
X-RAY DIFFRACTIONr_angle_refined_deg1.742.0154903
X-RAY DIFFRACTIONr_angle_other_deg0.90837658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023917
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02673
X-RAY DIFFRACTIONr_nbd_refined0.2220.2748
X-RAY DIFFRACTIONr_nbd_other0.2470.23870
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.22092
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2422
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.52153
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51423479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.37631463
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8464.51424
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.212 241
Rwork0.199 4690

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