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- PDB-7qak: Mus Musculus Acetylcholinesterase in complex with 7-[(4-{[benzyl(... -

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Basic information

Entry
Database: PDB / ID: 7qak
TitleMus Musculus Acetylcholinesterase in complex with 7-[(4-{[benzyl(methyl)amino]methyl}benzyl)oxy]-4-(hydroxymethyl)-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 / nuclear envelope / presynaptic membrane / 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-5IK / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.60000329418 Å
AuthorsEkstrom, F.J. / Forsgren, N.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: 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.
History
DepositionNov 17, 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

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,20923
Polymers119,5292
Non-polymers3,68021
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint62 kcal/mol
Surface area38140 Å2
Unit cell
Length a, b, c (Å)78.453, 112.710, 226.704
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, 6 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59764.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 32-574 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell line (production host): HEK293 / 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.: 4 / 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, 146 molecules

#3: Chemical ChemComp-5IK / 4-(hydroxymethyl)-7-[[4-[[methyl-(phenylmethyl)amino]methyl]phenyl]methoxy]chromen-2-one


Mass: 415.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#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-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 4.19 Å3/Da / Density % sol: 70.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.6→49.0197 Å / Num. obs: 62618 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 58.5166482128 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07385 / Net I/σ(I): 20.13
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 0.5853 / Num. unique obs: 6183 / CC1/2: 0.989

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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: 2.60000329418→49.0197 Å / SU ML: 0.309221465582 / Cross valid method: FREE R-VALUE / σ(F): 1.3378394356 / Phase error: 26.3701854478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223619299372 1246 1.99506837032 %
Rwork0.18993512215 61208 -
obs0.190581423579 62454 99.6203662349 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.6205896567 Å2
Refinement stepCycle: LAST / Resolution: 2.60000329418→49.0197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8347 0 247 129 8723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003084517525668891
X-RAY DIFFRACTIONf_angle_d0.69484435134412109
X-RAY DIFFRACTIONf_chiral_restr0.04911473579051292
X-RAY DIFFRACTIONf_plane_restr0.005522905074891576
X-RAY DIFFRACTIONf_dihedral_angle_d10.47052125587094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.60000329418-2.70410.3114814686491500.2554710987146686X-RAY DIFFRACTION99.4038098008
2.7041-2.82720.3266072807171330.2602952879296649X-RAY DIFFRACTION99.0217550007
2.8272-2.97620.3272786721471350.2523394635676712X-RAY DIFFRACTION99.231884058
2.9762-3.16260.2777265959631470.2371785724816705X-RAY DIFFRACTION99.5351539802
3.1626-3.40680.2669456718831280.2277829288786789X-RAY DIFFRACTION99.8844765343
3.4068-3.74950.2462395251361380.1945508328326784X-RAY DIFFRACTION99.8701486077
3.7495-4.29180.1975449414741410.1643485008856839X-RAY DIFFRACTION99.9713549126
4.2918-5.40610.1674874970081340.1515740377146889X-RAY DIFFRACTION99.8862181766
5.4061-49.01970.1888758250151400.1783694209377155X-RAY DIFFRACTION99.7538629837
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)
11.327917998340.024519484588-0.1550833661261.230427253-0.4532998218033.73112672187-0.10773416632-0.133673769658-0.008004169592070.1697622173530.012648333011-0.08921026340420.1638820928790.05448864177650.1023266916090.4651711046270.009700916856070.02206125950010.3530551020220.03081627164290.39643095369130.97050771211.549152803128.3958759297
25.538522325711.830502059890.05669195119131.36341418504-0.1165453015972.71250160689-0.1347394975860.347746238289-0.266635961492-0.0822913526570.00972566780875-0.2894699857310.2412851680730.3841059596710.1305561636590.5374854862570.1012389205530.06171889325140.4332261331090.03707230846150.39376604489241.698017113810.57201707811.0946456538
31.38367934718-0.189446169587-0.07589782554191.60114148579-0.4618739970723.9995655386-0.08506525932010.137362714652-0.045330780651-0.09654452616780.008955833357280.1825399083220.0746014511141-0.3516214682250.06866775975560.373996460558-0.0608661287394-0.000458772540760.4634839951810.002477763901780.44846354329518.603735910817.58675848876.54453762471
47.270558564340.4480177467314.609253994029.39733426808-1.809894124116.88953855279-0.1363627280440.0569763905731-0.5301208777410.3784143093590.2040440586670.6971351462970.644426361237-1.79447492823-0.0006442041585910.593636562597-0.2777439117750.07015728805930.7057496254050.03238521887520.6298515432776.954249116751.5190704867514.0715539041
52.22797663539-2.15920766212-2.380385948363.450154931393.104340324963.359123201820.055176858453-0.338618693842-0.0189650621627-0.295278047664-0.04020059066150.1060055147330.03293689588750.1930247373590.08899211573190.570820437035-0.0484433402985-0.09579444137570.813500639431-0.0009824440134570.44463253970517.42928985956.55947853868-0.761099916138
66.84601019248-0.907886314701-1.678837198251.649517378620.5136115150454.26294379290.1049746636330.4803394123850.235868812085-0.304746586137-0.1444878729490.389270875144-0.10631110075-0.6563884443650.122008714380.6508234107450.0266557189012-0.1314706630170.56283118733-0.1322397497770.556715933566-3.362531477485.63076496788-61.4976128902
71.28285333272-0.1138860728260.2671060872582.355285398680.4572331652023.877889733160.09921718962070.195490069341-0.160951645311-0.180216986378-0.2525012837180.4676300978080.351121726367-0.4099576776930.1366840089450.455386395311-0.0298415982552-0.07365626751920.485938965038-0.1151144909090.5143863864122.155769035340.961991880982-51.1385265338
89.7148849354-6.710847446374.949087672496.04042352426-4.225423263415.560972389330.3602617183610.5398295585290.278649026013-0.512113786254-0.4646931020070.0188749708516-0.2248490043390.2492303750860.05641538016650.543361867907-0.0242697466722-0.02728708101460.509628290279-0.06733266645590.53225935546216.38143898887.23082454564-54.7411505851
92.91833268232-1.035987808950.1930748115882.71306550429-0.007953576993393.499628232520.1385850438140.1771275675280.0738589865820.00402774245602-0.20131101087-0.0277479022365-0.1830725075890.3068287489450.03923214096350.382137860984-0.045833799199-0.01881371427130.346584127039-0.06694419183340.33108613496713.82244527338.50021815794-44.7044752415
102.8795170006-1.08765820618-1.578027714413.40242537272.275747065384.542186995820.03885204462110.233625683216-0.1559739571360.009356486754430.0438456028239-0.2043518081820.3598629694370.53668868364-0.0399166454530.7303040743510.107351619533-0.1089233929080.593303743466-0.05434038852280.56524346228922.600285759-9.80591697288-46.875290237
115.00786191227-2.58008746421-1.672328761432.260033098931.437421116173.711263143510.2509310197120.3038441099570.633143755349-0.127683761021-0.186597618648-0.217254893041-0.3492733696040.492372307975-0.06087539213690.492397332222-0.0515287661046-0.06323820027540.483839538537-0.04898126162310.47562302756817.987850294914.4262083231-39.9576532037
125.044250251610.2881720300020.8484561227993.1852683334-0.2863158563843.279817982710.189670816594-0.168711933544-0.2908068714540.526851385389-0.0205058489261-0.01848920050990.6911637910840.0351941235727-0.1653222714280.926292286636-0.0311791252220.0266059790690.524737730192-0.02626402489430.46493316477113.8263793725-6.20076896573-21.4696298943
131.749254024630.08704626099550.3988691149811.87079114612-0.6141490883922.981529226390.159355919461-0.2107472671640.006785811394420.281974860012-0.1867322759030.3645544845360.127663432738-0.3750258111880.024395324740.497243559018-0.0705995524010.07759898088580.533977989139-0.1694593322630.4881966561570.483294268335.80065233302-28.7948422952
146.619248525543.15755611821-0.4761413862278.76331637665-1.12704475295.668197396450.0966330641358-0.2837246348830.993070761339-0.2675572176480.06886811735740.889439989313-0.567000281187-0.43054551397-0.2100044278240.7389987618040.06364951530020.05065515499780.545186991885-0.158626225380.677809252632-1.3845049291522.4299272796-28.5810430788
154.455575765550.4133264783883.121302334761.691455326840.5461208193652.77828740640.163639031003-0.281858707185-0.1207830518480.156275319-0.1363227086180.07695649132090.0891468777230.199789733494-0.006103032190770.699220966605-0.06820564596510.04564634117290.628513618962-0.05526119082860.41662442584712.983144360811.4478963613-21.3818304657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 331 )
3X-RAY DIFFRACTION3chain 'A' and (resid 332 through 486 )
4X-RAY DIFFRACTION4chain 'A' and (resid 487 through 513 )
5X-RAY DIFFRACTION5chain 'A' and (resid 514 through 542 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 45 )
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 158 )
8X-RAY DIFFRACTION8chain 'B' and (resid 159 through 186 )
9X-RAY DIFFRACTION9chain 'B' and (resid 187 through 255 )
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 298 )
11X-RAY DIFFRACTION11chain 'B' and (resid 299 through 331 )
12X-RAY DIFFRACTION12chain 'B' and (resid 332 through 382 )
13X-RAY DIFFRACTION13chain 'B' and (resid 383 through 486 )
14X-RAY DIFFRACTION14chain 'B' and (resid 487 through 513 )
15X-RAY DIFFRACTION15chain 'B' and (resid 514 through 543 )

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