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- PDB-5p8w: Crystal Structure of COMT in complex with [5-(2,4-dimethyl-1,3-th... -

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Basic information

Entry
Database: PDB / ID: 5p8w
TitleCrystal Structure of COMT in complex with [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methanamine
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION
Function / homology
Function and homology information


: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process ...: / response to olanzapine / response to risperidone / 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 / renal sodium excretion / developmental process / renal filtration / S-adenosylmethionine metabolic process / renin secretion into blood stream / catecholamine metabolic process / dopamine secretion / renal albumin absorption / habituation / artery development / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / response to angiotensin / fear response / short-term memory / 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 corticosterone / response to temperature stimulus / response to pain / glycogen metabolic process / negative regulation of dopamine metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / dopamine metabolic process / exploration behavior / response to stress / multicellular organismal response to stress / behavioral fear response / response to cytokine / response to amphetamine / learning / kidney development / negative regulation of smooth muscle cell proliferation / female pregnancy / visual learning / response to wounding / response to estrogen / response to toxic substance / regulation of blood pressure / cognition / multicellular organism growth / memory / cell body / response to oxidative stress / response to lipopolysaccharide / methylation / gene expression / vesicle / dendritic spine / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / FORMIC ACID / Chem-O01 / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of COMT complex
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Derived calculations / Structure summary / Category: pdbx_deposit_group / pdbx_struct_oper_list
Item: _pdbx_deposit_group.group_type / _pdbx_struct_oper_list.symmetry_operation
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_symmetry / _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_symmetry
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4May 1, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,42417
Polymers74,0833
Non-polymers1,34114
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-98 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.931, 176.379, 119.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-521-

HOH

21C-461-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 3 / 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 , 5 types, 378 molecules

#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-O01 / [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methanamine / 1-[3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5-yl]methanamine


Mass: 208.283 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H12N4S
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.38 Å3/Da / Density % sol: 63.6 %
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: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→88.19 Å / Num. obs: 64984 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.76 % / Biso Wilson estimate: 37.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.096 / Χ2: 1.002 / Net I/σ(I): 14.06 / Num. measured all: 439417
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
2.03-2.081.4621.2730934476547600.5581.5999.9
2.08-2.141.151.6630510463746290.6791.24999.8
2.14-2.20.9122.231624450645020.8090.98599.9
2.2-2.270.7282.7430755438543820.8470.78599.9
2.27-2.340.5523.629618426442630.9040.597100
2.34-2.430.454.2928094410641030.9350.48799.9
2.43-2.520.3615.1826015399339870.9460.39399.8
2.52-2.620.2866.525258382138170.9660.31199.9
2.62-2.740.2218.4326054368936870.9840.23999.9
2.74-2.870.17410.724644352135190.9890.18899.9
2.87-3.030.13113.8823305336233580.9920.14199.9
3.03-3.210.09418.3721259317831760.9950.10299.9
3.21-3.430.06824.1919386301030090.9970.074100
3.43-3.710.05331.8919739280128010.9980.057100
3.71-4.060.04636.0817632255425540.9990.05100
4.06-4.540.03642.1515725236723620.9990.0499.8
4.54-5.240.03542.4212827207920790.9990.038100
5.24-6.420.03840.912288177917790.9990.041100
6.42-9.080.02945.788779140314020.9990.03299.9
9.08-88.190.02457.3849718268150.9990.02698.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_2481refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.03→48.636 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML / Details: DTT crosslinks Cys 33 and 69
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3291 5.07 %random
Rwork0.1676 61651 --
obs0.1695 64942 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.73 Å2 / Biso mean: 49.1691 Å2 / Biso min: 24.59 Å2
Refinement stepCycle: final / Resolution: 2.03→48.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 80 364 5456
Biso mean--49.17 51.35 -
Num. residues----640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165253
X-RAY DIFFRACTIONf_angle_d0.8127075
X-RAY DIFFRACTIONf_chiral_restr0.048799
X-RAY DIFFRACTIONf_plane_restr0.005907
X-RAY DIFFRACTIONf_dihedral_angle_d14.8643210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.03-2.0590.37311600.308825242684
2.059-2.08970.32321200.29925522672
2.0897-2.12240.33471490.264225152664
2.1224-2.15720.30981110.255625432654
2.1572-2.19440.3041310.233225632694
2.1944-2.23430.25941440.225425392683
2.2343-2.27730.26291330.210725492682
2.2773-2.32370.25041360.205425472683
2.3237-2.37430.23571220.191425512673
2.3743-2.42950.24781410.191625612702
2.4295-2.49030.24681430.19625222665
2.4903-2.55760.24351270.184625752702
2.5576-2.63280.21581290.181125762705
2.6328-2.71780.2171290.181525602689
2.7178-2.81490.22931470.197225252672
2.8149-2.92760.27361300.20225762706
2.9276-3.06080.26031410.202325762717
3.0608-3.22220.21531560.187525522708
3.2222-3.4240.2171380.164625772715
3.424-3.68830.18691290.146325892718
3.6883-4.05930.16391300.127826002730
4.0593-4.64630.11911420.112126172759
4.6463-5.85230.16961400.136626362776
5.8523-48.65010.17341630.151427262889
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5821.18911.25797.95632.02322.5920.0057-0.3711-0.3060.8529-0.12230.78170.3225-0.20320.11660.38560.03580.13120.3490.0380.3971-24.168443.9038-4.2462
20.9322-0.1878-0.52440.3257-0.25621.46110.0912-0.16980.13350.11170.1202-0.01960.07590.1293-0.18350.38350.0080.07410.32480.00230.2977-12.335548.7893-12.5574
31.5853-0.5958-0.75871.7281.14062.50830.12250.19630.02290.0018-0.11270.328-0.3696-0.5426-0.01450.32530.11990.06320.40560.03450.3404-23.774748.3173-24.031
41.959-0.386-0.71881.24760.78861.84270.05420.3313-0.0595-0.128-0.02820.0751-0.1491-0.2254-0.04470.32280.04740.02850.3634-00.2656-12.346139.562-34.0256
51.42320.36020.0832.4846-0.2760.9552-0.06150.2094-0.0558-0.04060.2378-0.08970.1001-0.0974-0.21540.3692-0.05470.03270.3222-0.00460.2942-2.761120.7268-13.6397
6222222-3.149-19.218-11.278416.05896.1701-8.891813.593627.1441-3.06441.77010.1357-0.62852.22310.20741.80914.52150.6686-27.4201
71.62951.66890.31771.91180.88981.62960.0272-0.15610.25120.2666-0.10450.3184-0.1008-0.11570.02430.3513-0.0191-0.08660.38380.02790.41788.794825.9903-0.2089
81.05890.80710.62331.59270.01633.09090.00660.0048-0.16250.0723-0.0808-0.4437-0.01180.40890.06230.2505-0.0009-0.03740.32570.0040.377816.723420.0488-10.1511
90.5425-0.1623-0.11131.3406-0.43841.4518-0.02340.0565-0.15840.05340.11190.04190.1418-0.1018-0.08520.2767-0.0491-0.02510.3032-0.01760.2797-0.282320.0535-19.8334
107.95181.4959-1.11185.03-0.51395.15850.41880.62660.9932-0.70710.04680.62390.45340.6368-0.49390.5957-0.0035-0.14290.67760.08370.6581-25.059422.9899-20.081
113.1959-1.35230.04675.9429-0.66435.204-0.23760.3594-0.266-1.23260.280.55240.60750.35280.03950.7196-0.1087-0.12320.59850.00680.6116-21.712613.2015-18.4524
124.47010.1028-1.79052.1107-0.52186.26360.1640.2019-0.3981-0.10920.0060.69680.8299-0.1286-0.16670.5892-0.02820.00160.36920.09950.6989-23.49726.4046-3.6046
131.317-0.00070.6452.7568-0.46582.40250.0610.01620.02720.1060.08290.8023-0.1983-0.3684-0.1170.33890.04030.09750.37030.04970.6092-26.525922.2589-1.8231
142.07251.588-0.29182.966-0.7072.2379-0.2589-0.1226-0.05810.28670.1490.6828-0.1124-0.22540.11430.53150.02550.12170.42730.03630.5439-22.695919.36146.1539
150.8901-0.28010.57562.50590.05650.4416-0.0025-0.18360.07250.63550.08290.17740.0361-0.0695-0.06750.5060.00170.06090.38780.0580.3793-13.505412.50448.1649
161.7826-0.3552-0.52263.2571.03186.24080.19110.04620.22210.11260.28140.0941-0.11520.2376-0.29490.4305-0.02020.01540.33390.09230.3918-13.93354.7423-1.0458
17222222-2.1049-10.8227-3.095915.619-4.790419.49690.9666-8.34926.8911.20810.202-0.14991.7668-0.31122.0537-15.386610.710223.5374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )A2 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 57 )A17 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 143 )A58 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 195 )A144 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 215 )A196 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 216 )A216
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 70 )B3 - 70
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 143 )B71 - 143
9X-RAY DIFFRACTION9chain 'B' and (resid 144 through 215 )B144 - 215
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 21 )C3 - 21
11X-RAY DIFFRACTION11chain 'C' and (resid 22 through 41 )C22 - 41
12X-RAY DIFFRACTION12chain 'C' and (resid 42 through 57 )C42 - 57
13X-RAY DIFFRACTION13chain 'C' and (resid 58 through 129 )C58 - 129
14X-RAY DIFFRACTION14chain 'C' and (resid 130 through 143 )C130 - 143
15X-RAY DIFFRACTION15chain 'C' and (resid 144 through 196 )C144 - 196
16X-RAY DIFFRACTION16chain 'C' and (resid 197 through 215 )C197 - 215
17X-RAY DIFFRACTION17chain 'C' and (resid 216 through 216 )C216

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