[English] 日本語
Yorodumi
- PDB-5lr6: Crystal Structure of COMT in complex with [3-(2,4-dimethyl-1,3-th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lr6
TitleCrystal Structure of COMT in complex with [3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5-yl]-(4-phenylpiperazin-1-yl)methanone
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-731 / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEhler, A. / Lerner, C. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of COMT in complex with [3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5-yl]-(4-phenylpiperazin-1-yl)methanone
Authors: Lerner, C. / Rudolph, M.G.
History
DepositionAug 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,21816
Polymers98,7774
Non-polymers2,44112
Water4,378243
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3054
Polymers24,6941
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3054
Polymers24,6941
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3054
Polymers24,6941
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3054
Polymers24,6941
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.983, 103.621, 78.409
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Catechol O-methyltransferase / Catechol-O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 4 / 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 BL21(DE3) (bacteria) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical
ChemComp-731 / [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone


Mass: 367.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21N5OS
#3: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: AMMONIUM SULPHATE, CHES, PH 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.3→46.94 Å / Num. obs: 50076 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.36 % / Biso Wilson estimate: 45.59 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.51
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.3-2.361.0181.330.742199.6
2.36-2.420.6881.840.789199.8
2.42-2.490.6032.10.834199.7
2.49-2.570.4572.570.876199.2
2.57-2.660.4042.910.909199.7
2.66-2.750.3353.680.941199.5
2.75-2.850.2734.610.956199.5
2.85-2.970.2055.580.979199.4
2.97-3.10.1527.220.985199.5
3.1-3.250.138.380.984199.2
3.25-3.430.09610.220.991199
3.43-3.640.08611.390.994199.2
3.64-3.890.07913.360.992199.2
3.89-4.20.06414.970.995198.7
4.2-4.60.0616.030.994198.6
4.6-5.140.05615.570.995198.5
5.14-5.940.0615.160.996199.4
5.94-7.270.05415.970.996199.6
7.27-10.290.04718.260.996197.9
10.29-46.940.04620.860.997198.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.3→46.938 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.31
Details: twinned p21 with beta=90. P222 pseudo-symmetry, but structure will not refine in any orthorhombic setting, although the data reduce nicely in P222. Best higher metric symmetry space group ...Details: twinned p21 with beta=90. P222 pseudo-symmetry, but structure will not refine in any orthorhombic setting, although the data reduce nicely in P222. Best higher metric symmetry space group based on MR LLG. Pseudotranslation in P21 is at 0.038 0.500 0.548. Ligand can be placed with confidence.
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 2571 5.15 %random
Rwork0.1957 ---
obs0.2035 49921 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.65 Å2 / Biso mean: 39.0013 Å2 / Biso min: 4.63 Å2
Refinement stepCycle: final / Resolution: 2.3→46.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 160 243 7062
Biso mean--32.31 29.7 -
Num. residues----852
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)
11.93850.5322-0.65741.4095-0.48751.060.0133-0.49730.24930.33020.1822-0.2662-0.14410.28590.05770.2156-0.0355-0.08390.69960.02080.256126.35147.246234.8922
22.41760.641-1.30262.1583-0.222.53660.0316-0.21340.5730.0225-0.0891-0.0205-0.30020.0726-0.1610.12350.0402-0.03670.702-0.05320.30317.92414.375732.5998
32.22340.07620.35252.00980.3494.18740.1723-0.14730.1134-0.0497-0.2567-0.2674-0.4278-0.1727-0.09480.22530.014-0.05080.5519-0.00530.437917.356517.042620.2504
41.17750.3143-0.36920.65150.43272.0476-0.0985-0.1223-0.0529-0.0789-0.03540.01570.1695-0.27750.02830.09620.0042-0.04590.53020.00460.215817.21094.115714.2024
50.91360.54560.56044.17131.97814.91150.13170.01130.084-0.730.14950.2589-0.2787-0.28060.01860.24340.0387-0.01390.49650.06970.252220.27518.48293.5098
62.87251.55620.19733.90732.06863.87410.1875-0.1115-0.0311-0.18220.3807-0.141-0.2552-0.0398-0.07270.17660.0388-0.09850.4455-0.01290.290819.166417.52876.8071
71.89830.0191-0.23452.3730.47593.04150.1944-0.6148-0.21290.11070.17970.40720.2531-0.68570.06830.2049-0.0496-0.01580.6151-0.0080.25796.2476-7.475774.0329
83.54550.2521.0043.0771.18554.19380.1966-0.3931-0.58560.4273-0.2077-0.14961.0858-0.1095-0.09930.3278-0.0349-0.02480.56930.01870.213514.7819-14.651771.7441
90.9522-0.59480.15272.97030.68894.96510.0261-0.56-0.46160.5321-0.21010.06440.4476-0.2952-0.07650.3692-0.00720.02190.61690.03010.310516.684-17.973359.189
101.4242-0.0559-0.15191.1860.25842.49830.1045-0.0451-0.01130.0073-0.0484-0.1497-0.1490.15750.00120.1189-0.0042-0.01440.5467-0.0150.193515.4566-4.418653.393
111.37360.32760.37163.9317-1.6934.11720.13910.099-0.3997-0.48830.0649-0.21810.35670.052-0.04330.21110.0328-0.03550.625-0.07210.226112.4947-18.892342.8572
123.16640.8955-0.34754.0039-1.3685.6350.2355-0.12060.12960.07720.15550.14380.5587-0.1934-0.14630.2110.0228-0.06240.538-0.0150.206412.1376-19.047548.724
132.6138-0.03950.47042.20640.35424.46870.1990.38980.5833-0.129-0.1050.0904-0.65930.01550.15160.22260.0394-0.00570.6320.01920.264746.31911.83241.8483
140.71240.0454-1.31813.1937-0.02254.09750.10420.4520.3369-0.0194-0.1539-0.2595-0.87290.16220.09840.2682-0.04660.05620.60620.06180.293350.906917.959615.3685
151.1183-0.17760.07250.9433-0.21773.272-0.02280.1348-0.04650.0694-0.0443-0.03620.06870.23240.07370.1213-0.0045-0.01740.49670.01020.216950.90834.757421.258
162.1496-0.46380.50493.621-2.0646.8644-0.3386-0.19770.10810.77640.1236-0.0951-0.64-0.02360.14140.3356-0.0479-0.04990.5105-0.11110.259447.721119.147531.8848
173.3287-0.48710.06054.2383-1.14415.6057-0.10780.46630.1118-0.0496-0.12070.5552-0.6116-0.31010.04830.2606-0.1137-0.14420.4183-0.00510.39147.772318.936126.9778
181.58690.3766-0.13852.17960.12874.59040.09020.3575-0.0649-0.05620.1418-0.06350.15150.53920.04630.22590.0481-0.03170.4398-0.06620.233261.8827-6.894639.8263
193.54050.36451.03862.9555-1.26954.53890.1140.0301-0.5569-0.6197-0.05250.19540.6347-0.2792-0.13210.2857-0.0539-0.04160.5135-0.01920.192253.4878-14.031342.0966
203.78780.0734-1.82691.86320.3435.83830.0365-0.0617-0.08650.2628-0.2828-0.11770.6901-0.0822-0.13080.3413-0.0143-0.07490.43270.07710.343153.3084-16.497554.511
211.12980.2987-0.31420.88730.14533.2810.0369-0.09590.0159-0.05410.00530.1169-0.1507-0.22090.00750.1220.0089-0.04150.49590.00870.212252.7178-3.755860.5133
222.3933-2.4559-1.95924.11731.46637.95530.2686-0.52830.06850.48140.1294-0.08990.35480.44730.00810.3109-0.0541-0.09690.58720.02620.287657.437-14.833876.185
231.06420.2974-1.27524.0802-0.50254.748-0.08490.6225-0.2854-0.46720.21-0.41460.95680.3290.33160.27390.00880.10610.8685-0.03370.317957.2356-22.054163.04
241.09490.48750.332.05340.1094.7084-0.0101-0.29370.08760.357-0.09070.03160.3088-0.23220.04440.2453-0.1021-0.02710.43170.08920.194352.8419-16.242369.5636
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 35 )A17 - 35
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 57 )A36 - 57
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 176 )A58 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 198 )A177 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 216 )A201 - 216
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 16 )B2 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 35 )B17 - 35
9X-RAY DIFFRACTION9chain 'B' and (resid 36 through 57 )B36 - 57
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 176 )B58 - 176
11X-RAY DIFFRACTION11chain 'B' and (resid 177 through 198 )B177 - 198
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 216 )B199 - 216
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 35 )C3 - 35
14X-RAY DIFFRACTION14chain 'C' and (resid 36 through 57 )C36 - 57
15X-RAY DIFFRACTION15chain 'C' and (resid 58 through 176 )C58 - 176
16X-RAY DIFFRACTION16chain 'C' and (resid 177 through 198 )C177 - 198
17X-RAY DIFFRACTION17chain 'C' and (resid 199 through 217 )C199 - 217
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 16 )D2 - 16
19X-RAY DIFFRACTION19chain 'D' and (resid 17 through 35 )D17 - 35
20X-RAY DIFFRACTION20chain 'D' and (resid 36 through 57 )D36 - 57
21X-RAY DIFFRACTION21chain 'D' and (resid 58 through 176 )D58 - 176
22X-RAY DIFFRACTION22chain 'D' and (resid 177 through 188 )D177 - 188
23X-RAY DIFFRACTION23chain 'D' and (resid 189 through 202 )D189 - 202
24X-RAY DIFFRACTION24chain 'D' and (resid 203 through 215 )D203 - 215

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more