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- PDB-7qb4: Mus Musculus Acetylcholinesterase in complex with 7-[(1-benzylpip... -

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Basic information

Entry
Database: PDB / ID: 7qb4
TitleMus Musculus Acetylcholinesterase in complex with 7-[(1-benzylpiperidin-3-yl)methoxy]-3,4-dimethyl-2H-chromen-2-one
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Inhibitor / complex
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / 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-9YU / Chem-AJ9 / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.50001104077 Å
AuthorsEkstrom, F.J. / Forsgren, N.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other government Sweden
Citation
Journal: Acs Med.Chem.Lett. / Year: 2022
Title: Dual Reversible Coumarin Inhibitors Mutually Bound to Monoamine Oxidase B and Acetylcholinesterase Crystal Structures.
Authors: Ekstrom, F. / Gottinger, A. / Forsgren, N. / Catto, M. / Iacovino, L.G. / Pisani, L. / Binda, C.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionNov 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)123,44127
Polymers119,5292
Non-polymers3,91225
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint77 kcal/mol
Surface area38570 Å2
Unit cell
Length a, b, c (Å)79.406, 111.048, 227.092
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, 5 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.: 3 / Source method: obtained synthetically / 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, 145 molecules

#3: Chemical ChemComp-AJ9 / 3,4-dimethyl-7-[[1-(phenylmethyl)piperidin-4-yl]methoxy]chromen-2-one / 7-[(1-benzylpiperidin-3-yl)methoxy]-3,4-dimethyl-2H-chromen-2-one


Mass: 377.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#7: Chemical ChemComp-9YU / 2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol


Mass: 340.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32O8
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.22 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 30% (v/v) polyethylene glycol 750 monomethylether, 100 mM HEPES, pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9797 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.5→46.191 Å / Num. obs: 70307 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.5079911089 Å2 / CC1/2: 0.891 / Rmerge(I) obs: 0.2744 / Net I/σ(I): 9.05
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.63 / Num. unique obs: 6926 / CC1/2: 0.676

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.50001104077→46.191 Å / SU ML: 0.254836318421 / Cross valid method: FREE R-VALUE / σ(F): 1.33568768175 / Phase error: 26.7739461301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216988384936 1396 2.00100336845 %
Rwork0.184216151478 68369 -
obs0.184851813327 69765 99.2163945617 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.911917035 Å2
Refinement stepCycle: LAST / Resolution: 2.50001104077→46.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8349 0 233 123 8705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004589810629718877
X-RAY DIFFRACTIONf_angle_d0.73003388802512081
X-RAY DIFFRACTIONf_chiral_restr0.04634154967891289
X-RAY DIFFRACTIONf_plane_restr0.005051569502181574
X-RAY DIFFRACTIONf_dihedral_angle_d16.11802889175227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.50001104077-2.58940.2886199386921450.2626204071996649X-RAY DIFFRACTION98.0941380306
2.5894-2.6930.290821602361470.2421102265536685X-RAY DIFFRACTION98.4438040346
2.693-2.81560.3014588901441340.2383199471896701X-RAY DIFFRACTION98.345323741
2.8156-2.9640.3158696623981390.2285181076156765X-RAY DIFFRACTION99.1811521333
2.964-3.14960.2359568460421490.2193184487376751X-RAY DIFFRACTION99.0383235252
3.1496-3.39280.2731914893521230.2120402867666846X-RAY DIFFRACTION99.713836028
3.3928-3.73410.2367418453791470.1916478174776847X-RAY DIFFRACTION99.6722245974
3.7341-4.27410.1912059615381340.1623322603646928X-RAY DIFFRACTION99.9009760928
4.2741-5.38350.1481407507321360.1461884094556970X-RAY DIFFRACTION99.9577999719
5.3835-46.1910.1954940035961420.1722231961247227X-RAY DIFFRACTION99.7428262047
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)
11.15616027505-0.07988732334670.2004279057951.60756466249-0.2009767276933.14334567561-0.0599343033003-0.2138348799870.03098673093490.240018745290.0126012330265-0.01396944528630.0922047864552-0.0209567258540.05200680994980.5126708934410.0160911211069-0.01569350773890.4466543118090.02870725466890.38705504524631.191866056312.147111357929.7719169729
24.329958675371.273775403790.2167278935072.00478372858-0.02887225061852.83024595624-0.08861588334030.263652093753-0.36035177239-0.09032401491760.0497606477108-0.2086380652660.4139867660660.2142734447120.03245241935840.4921093009520.1010741623510.0370496257930.4052659872290.01247798550090.37512015779839.92613598968.374052345311.8401794384
31.311359102561.7933560655-0.7858929264017.77575029654-2.952136721564.480983083650.056402588988-0.02320553402360.1679632552390.404674434964-0.0168879596529-0.0204860213944-0.5729214187570.0523685058827-0.0140717003490.40451213691-0.037693773749-0.02103704829270.5230027925980.03136789040890.43768122050923.806979848622.23754501941.29191250346
41.46977309452-0.3312806500680.1808576140022.056442520960.1592357350955.34392646336-0.04256252596180.0693202214035-0.0359697708864-0.1561032008660.01741030955540.317516998072-0.00392553770121-0.5942355740730.02319234657820.331085738262-0.0489190584194-0.03120674739280.4561817268780.01319607590540.42865348926416.791799042515.13990231648.55655001752
52.64759284607-0.7081316166842.687174541944.65129717075-0.8772219271567.90999783968-0.125886637975-0.000834353263472-0.735734158410.294581552980.127743854550.8549220410450.977074674173-1.819782441940.07768323309570.689604199703-0.3335957194290.04949799367150.899996238450.08037332251520.6870846936746.779513554331.3431650948613.9326827728
63.5130142322-1.19600562586-3.255713403372.637853425581.887773021744.835984562240.16547005283-0.0009524002139480.0121718737785-0.359866684432-0.05416248236860.1343154523840.1796633308070.126622673679-0.05946027104220.630593247831-0.0213694007125-0.1372759712150.7356115170520.002023189317470.46127267240317.42159686266.34888518911-0.859910959949
76.98858216136-1.77530084195-4.699616990922.949301697221.849058014856.555450762720.06453145092510.6886144805260.158614053051-0.41005689375-0.1660872382410.274400316502-0.0465611696488-0.9471887910240.07616775693870.624410520212-0.0178175725277-0.09574901226210.620852109582-0.1212942740390.473907448929-3.678255860195.90262941837-61.6107341425
80.629115041307-0.04000741500750.03459488814062.421476474940.1801937390263.192797815310.1905954080760.266334185637-0.28529842063-0.121894927167-0.2145784220040.310557266450.54947240719-0.3051966266930.00339339815580.542158030235-0.0785244318536-0.06611309259050.579039289176-0.08202297694830.4070581499121.831282972880.532383566469-51.630649382
92.84836065837-1.742974118130.08937283599523.277056812570.2424175329282.837172770260.2217687771250.2832806651050.0625425147842-0.247659684411-0.136848446415-0.193423313401-0.1120342121240.273092652044-0.06944429706860.455305660892-0.0382872711620.003574292773160.505855232941-0.05401013798750.35319251093513.51820197157.88903042435-48.4165626093
102.70088955929-0.789013100288-1.047031999633.263109256021.55339144933.311848663420.08404322264710.132892926363-0.153025587632-0.09473672017220.0917389910498-0.342768317670.3053514361580.602343132479-0.1595382565390.548480291040.0415682877908-0.1185057780880.559520776667-0.0470587978880.35785498133920.97447578420.955533114222-43.8711713395
114.388913207890.6287812212710.1735343915274.498512269250.1006589047682.459085746670.314725565282-0.235141518474-0.6105682016810.649328553114-0.116276480772-0.02557789875470.847608432560.0906846510217-0.2241035572770.8999413840670.00171143555963-0.05485471955520.442166201121-0.01182180786310.42548568170913.9031533467-6.41967504165-21.6873940592
122.396401814170.195092274640.4765974168091.54837256139-0.2092131956352.990804857350.200417295075-0.260623278333-0.1377405629120.235651627759-0.1038035483250.2379732912020.265150466924-0.351953979819-0.1055089935260.564360126216-0.0765920276030.02774563217490.487173940416-0.1037376071230.4661470519780.5278394131935.57394452014-28.9795331007
139.958194741111.548806560761.761522059334.08546811234-1.791021917526.37764000712-0.131671234771-0.5486402900411.05618691080.2058186935720.02469010489840.409932894306-0.682345146812-0.4687146766960.1525703423910.7457367369550.06374685608520.02515882522710.452883250102-0.1023128790130.522370045879-1.3306811423522.1726898435-28.6144976017
145.22232685393-0.5230942091492.720049570781.428604327970.215349938732.696325976790.1481943906640.244376905663-0.2365695665750.0652785346195-0.09800226634920.02450056217310.2588842037880.278859214489-0.03399749896680.782698645195-0.0405642342308-0.02298963761760.641850551562-0.04159943533530.39695728544212.992562857411.1592966371-21.4551317108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 324 )
3X-RAY DIFFRACTION3chain 'A' and (resid 325 through 366 )
4X-RAY DIFFRACTION4chain 'A' and (resid 367 through 486 )
5X-RAY DIFFRACTION5chain 'A' and (resid 487 through 513 )
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 542 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 45 )
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 141 )
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 255 )
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 331 )
11X-RAY DIFFRACTION11chain 'B' and (resid 332 through 382 )
12X-RAY DIFFRACTION12chain 'B' and (resid 383 through 486 )
13X-RAY DIFFRACTION13chain 'B' and (resid 487 through 513 )
14X-RAY DIFFRACTION14chain 'B' and (resid 514 through 543 )

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