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- PDB-6td2: Mus musculus Acetylcholinesterase in complex with N-(2-(diethylam... -

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Basic information

Entry
Database: PDB / ID: 6td2
TitleMus musculus Acetylcholinesterase in complex with N-(2-(diethylamino)ethyl)-1-(4-(trifluoromethyl)phenyl)methanesulfonamide
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Complex / Inhibitor
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / laminin binding / collagen binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-ETE / Chem-N2K / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsForsgren, N. / Ekstrom, F.
Funding support2items
OrganizationGrant numberCountry
Other government
Swedish Research Council
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu.
Authors: Andersson, C.D. / Mishra, B.K. / Forsgren, N. / Ekstrom, F. / Linusson, A.
History
DepositionNov 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,18419
Polymers119,5292
Non-polymers2,65517
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.957, 111.957, 227.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59764.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 185 molecules

#3: Chemical ChemComp-N2K / ~{N}-[2-(diethylamino)ethyl]-1-[4-(trifluoromethyl)phenyl]methanesulfonamide


Mass: 338.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21F3N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30 % (w/v) PEG750MME 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.041 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.8→28.9 Å / Num. obs: 50138 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.4038821796 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.494 / Num. unique obs: 7255

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JO6

1jo6


Resolution: 2.8→28.851 Å / SU ML: 0.30406205041 / Cross valid method: FREE R-VALUE / σ(F): 1.33784944444 / Phase error: 23.8261974636
RfactorNum. reflection% reflection
Rfree0.215251914175 981 1.96408192684 %
Rwork0.174582101838 --
obs0.175365448692 49947 99.0010108818 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.8911291687 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8327 0 173 170 8670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007612529948818823
X-RAY DIFFRACTIONf_angle_d0.99364661748612038
X-RAY DIFFRACTIONf_chiral_restr0.05714342593851285
X-RAY DIFFRACTIONf_plane_restr0.007422598379661572
X-RAY DIFFRACTIONf_dihedral_angle_d11.31840396517094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94750.3099697180511370.2646002301266922X-RAY DIFFRACTION99.6049103993
2.9475-3.1320.2781303885381550.2364302410136906X-RAY DIFFRACTION99.5488509798
3.132-3.37350.2804235142921300.2270553182026974X-RAY DIFFRACTION99.7472620051
3.3735-3.71230.2438139166311440.1777046561077015X-RAY DIFFRACTION99.7075208914
3.7123-4.2480.2220164401611320.1520500976916994X-RAY DIFFRACTION99.3724724585
4.248-5.34650.1436972160761400.1310267288917049X-RAY DIFFRACTION98.8042880704
5.3465-28.850.1779830847451430.1595036646547106X-RAY DIFFRACTION96.3834596463
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)
13.86258575264-1.05555179246-0.590963696831.97264444252-0.939113585985.66248064636-0.265303029985-0.5073841525140.09112250772050.5785119737670.16533128130.0197414764322-0.101832787916-0.07591100440390.009425203457920.452500294194-0.0147966073736-0.03859907229040.277858034952-0.0165003793730.26040528020729.988664734813.059107567941.4656525467
22.619656845430.174222009823-0.4940058471471.58718994098-0.04495931542512.62666029589-0.0806955854521-0.2970295034050.08817655310980.2128885748190.01581858464-0.0591401283954-0.03863762251740.1056674762670.0519865374180.307539624530.0326223038161-0.04109443099330.299746540308-0.0002683948593290.19914010703431.008076624715.901822013127.7083438699
31.751120957310.63267587729-1.226033848592.15731283628-0.7194786978264.94311590548-0.130124637234-0.169507711691-0.2862404635350.0482402309510.0779221347655-0.1305460212710.696579235743-0.03081947351910.05251429200840.3406899619510.0351552919158-0.02094437267820.2611375466160.04648962270270.26849538368532.154781632.9627822573721.1333862563
42.36528459174-0.8944030326512.7480522455.385853565981.592464654488.218972982240.1102440140930.234627919301-0.0376944907215-0.593534506587-0.349459122474-0.921390357480.006975633927141.270389159160.2154178281860.2957225652520.0399327574780.08111085257340.5673344326120.124715663610.43716234914354.03385690813.89551557612.2104914886
53.954535537121.532193499192.319816888974.109723490221.784891505993.64272977727-0.02517663082020.0922659927734-0.269164822444-0.00897910083932-0.0265028623027-0.2318458244060.3922315950260.1793337611340.04243966039480.367356256680.0874925062110.1175665562940.4053238509570.06010694177480.21501082314837.24183373428.010500697149.32667873987
61.93929842115-0.332215306964-0.06165237005921.95812450709-0.7380075738454.10139348027-0.01852442781880.09708063192220.0487649813755-0.127372750790.08340574392760.1957124720560.0685676571734-0.376133602175-0.05585909192160.208936193741-0.0268224485902-0.04058330409860.3217688681560.003582828204620.25406397272919.043303581417.0340637716.23508782144
75.225610529230.2284727712843.905317485798.49293048047-2.037295790014.009895434770.020451867739-0.119994597952-0.6595673253540.2161363364330.3065354532771.09157501570.541466194607-1.18298609541-0.1739802810360.45290078897-0.230409407684-0.006056070925790.5551663562690.08318598864580.5294367709167.069758765831.4045855217413.4499775915
83.08522611664-1.44330815831-5.041837321043.115088733743.245325718928.627803323710.01064256557490.108708309479-0.127703650478-0.4793554977170.02110105466770.2709242375780.0445685320657-0.215346246980.003105477162360.457240940744-0.001459435888-0.1765108637320.6728354830990.06901227892750.3262743909417.65966173916.45479308916-1.30236500891
96.82459455735-1.1689827832-2.964762012032.220226589330.6507038397385.675706269180.06681983884470.7153611464660.0899822632171-0.282248797908-0.175866203240.32626591313-0.00765552201404-1.016272418740.09076255049390.4891443225740.0315744370701-0.09839644842820.495355406795-0.1430855063910.37058180383-3.539175570996.37288373024-62.0030322926
100.769904182377-0.496153303269-0.3077580776032.225450607940.398015405863.321428158870.2108641878790.215085622761-0.130556533907-0.115690686151-0.2230437107550.120578901210.658586249031-0.0726512861586-0.04325991701790.471928830767-0.0429336210747-0.07869744807680.621499991876-0.07447556213850.3023938370135.33430919148-4.03955376657-53.1765683737
112.396797616590.471818943127-0.78109162852.747585828461.02175457712.124049883760.02236499501870.5916937395940.0713905643347-0.389757475879-0.2734641007190.4460143149580.166535944789-0.3088774568880.1976449381630.4490484310970.0794199235199-0.1310435368390.595652112109-0.108540425630.300126263963-1.206560783546.0203862176-53.9495508564
124.95566429622-0.9845068138861.54989064771.680451930120.4738366387481.779118548140.1905277718710.629878412387-0.173477790774-0.114540439748-0.1752946901840.05448539223690.1257906701610.0186597387344-0.03906986573940.398250699614-0.00609301375145-0.02119774272660.420815788564-0.04631175441490.205652774687.55983202143.05520837504-48.9757415155
132.11399680169-1.214421909930.07964298220022.954662776340.7906205291173.050198724370.1079971987820.197425220724-0.04234415473880.006202342476610.0314404851979-0.2622992131410.1713598917760.528037961569-0.1328393963150.3416816146140.0212880461097-0.02167526300320.479759492367-0.04290488430540.24011685655317.27852830254.63149841262-46.6304274886
142.64219304839-2.597841990910.7146935204545.76550018003-2.209882814185.600541154490.0960024765219-0.0813186743227-0.171547018397-0.222207071492-0.0931003193464-0.1462824153580.4093360474740.009298979536590.01151608632840.319356293763-0.0568814357585-0.02342498440840.28382515457-0.07383952396230.2577077823348.565906678164.61410160889-31.6541100656
152.16960347613-0.4290556068440.6506479049731.95778232892-0.1166531392842.533216274440.154764153168-0.328758829671-0.2903258733570.297355706341-0.00540579272354-0.01270748116890.5928723589650.0338600843208-0.1527056363590.537022969672-0.0454360006408-0.03611779161860.403286210872-0.06081079271150.26120680465411.28545599951.31098185872-22.3776939854
161.84693923249-0.9241514225481.114829057075.96171840058-2.604452710435.94519971067-0.0774069382914-0.171032013211-0.06127106696920.2059964903120.1634591023860.4366232978920.186175652242-1.22570057436-0.06039425675980.349012489403-0.0372404358482-0.002784700126340.52400789659-0.132754477530.354762115973-7.493750677627.0100000139-35.5011914127
174.79044156922-0.808314951411.497940132864.99878930898-0.553112456892.233956976060.263918778144-0.4001140281640.7837929829050.4963792826730.01966744466890.736724446919-0.799232840471-0.582385632272-0.2557810888310.5161655166530.07900460313490.07588300987370.521023803543-0.005278922507480.417538891018-1.5603247685622.7729078154-28.9378755548
186.31312068234-0.3226846846395.370742330911.83154385108-0.3319693646354.62775466859-0.1007300042820.17040093337-0.1602900727210.327623976667-0.0935271283641-0.127071018582-0.04363458766140.3485425209190.215839317980.598936068252-0.0543333814620.008495741265280.466001097477-0.008150408801250.20930630369912.739073161611.7700923421-21.7536659898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 240 )
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 277 )
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 324 )
6X-RAY DIFFRACTION6chain 'A' and (resid 325 through 486 )
7X-RAY DIFFRACTION7chain 'A' and (resid 487 through 513 )
8X-RAY DIFFRACTION8chain 'A' and (resid 514 through 542 )
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 118 )
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 170 )
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 318 )
14X-RAY DIFFRACTION14chain 'B' and (resid 319 through 348 )
15X-RAY DIFFRACTION15chain 'B' and (resid 349 through 440 )
16X-RAY DIFFRACTION16chain 'B' and (resid 441 through 486 )
17X-RAY DIFFRACTION17chain 'B' and (resid 487 through 513 )
18X-RAY DIFFRACTION18chain 'B' and (resid 514 through 542 )

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