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- PDB-8orc: Mus Musculus Acetylcholinesterase in complex with AL237 -

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Basic information

Entry
Database: PDB / ID: 8orc
TitleMus Musculus Acetylcholinesterase in complex with AL237
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / neurotransmission / cholinesterase / inhibitor
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis ...acetylcholine metabolic process / serine hydrolase activity / choline metabolic process / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / laminin binding / side of membrane / synaptic cleft / 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 / hydrolase activity / cell adhesion / axon / endoplasmic reticulum lumen / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / 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
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / 2-METHOXYETHANOL / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / : / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEkstrom, F.E. / Linusson, A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Enzyme Dynamics Determine Potency and Selectivity of Inhibitors Targeting Disease-Transmitting Mosquitoes
Authors: Kumari, R. / Lindgren, C. / Kumar, R. / Forsgren, N. / Andersson, D. / Ekstrom, F. / Linusson, A.
History
DepositionApr 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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)121,61016
Polymers119,5292
Non-polymers2,08114
Water9,674537
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint19 kcal/mol
Surface area37490 Å2
Unit cell
Length a, b, c (Å)79.606, 112.113, 226.605
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 , 1 types, 2 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 / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase

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Non-polymers , 6 types, 551 molecules

#2: Chemical ChemComp-VY8 / 1-[2-(dimethylamino)ethyl]-3-(2-methoxyphenyl)thiourea


Mass: 253.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Chemical
ChemComp-MXE / 2-METHOXYETHANOL / 2-Methoxyethanol


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O4
#6: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 4.2 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 30% (V/V) POLYETHYLENE GLYCOL 750 MONOMETHYLETHER, 100 MM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.23 Å / Num. obs: 118925 / % possible obs: 99.81 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.21 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08429 / Rpim(I) all: 0.03368 / Rrim(I) all: 0.09086 / Net I/σ(I): 18.58
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.8978 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 11746 / CC1/2: 0.87 / Rpim(I) all: 0.3954 / Rrim(I) all: 0.9823 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.23 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 2379 2 %
Rwork0.1856 116374 -
obs0.186 118753 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8324 0 139 537 9000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00488761
X-RAY DIFFRACTIONf_angle_d0.722211936
X-RAY DIFFRACTIONf_chiral_restr0.0451272
X-RAY DIFFRACTIONf_plane_restr0.00611567
X-RAY DIFFRACTIONf_dihedral_angle_d19.03571267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.29571410.2926773X-RAY DIFFRACTION99.65
2.14-2.190.29121480.25746739X-RAY DIFFRACTION99.83
2.19-2.240.25061420.2386752X-RAY DIFFRACTION99.68
2.24-2.30.25211420.21716765X-RAY DIFFRACTION99.57
2.3-2.360.24851490.21376740X-RAY DIFFRACTION99.62
2.36-2.430.22041310.21046814X-RAY DIFFRACTION99.84
2.43-2.510.22061110.19966812X-RAY DIFFRACTION99.87
2.51-2.60.20831540.19766765X-RAY DIFFRACTION99.83
2.6-2.70.24191510.19856803X-RAY DIFFRACTION99.9
2.7-2.820.22571340.20236812X-RAY DIFFRACTION99.78
2.82-2.970.23511410.20846828X-RAY DIFFRACTION99.97
2.97-3.160.18721460.1986849X-RAY DIFFRACTION99.91
3.16-3.40.22031270.19296858X-RAY DIFFRACTION99.99
3.4-3.740.20081440.17176905X-RAY DIFFRACTION99.99
3.74-4.280.15041380.1476931X-RAY DIFFRACTION99.96
4.28-5.40.1531370.14176995X-RAY DIFFRACTION99.99
5.4-49.230.2321430.19067233X-RAY DIFFRACTION99.65
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)
14.33614190738-1.087325048630.331336332862.28549539284-1.211069655464.1891631347-0.177866096452-0.6896706037760.03155887590260.4415048203580.1788112188050.0132675593306-0.0813460290643-0.0680540436782-0.004658954224190.3867862689330.000369348165088-0.0302073007110.304385391341-0.003089556675390.25775915697429.819807577213.149139146541.5895670176
22.64961952255-0.1136393300330.2225780394410.7631438790531.117972814832.61908191776-0.217021548072-0.1329285428860.1948552582240.128558235261-0.0265561346611-0.182176799927-0.09613294071080.2873337292930.2677085319740.317895400292-0.042088290675-0.02517363803840.3293888882630.03719666711030.30885892753536.022344893419.665084943726.8071834486
34.28278066852-0.55820390278-0.3212454154761.149051864590.9174838733553.39943929782-0.199422343437-0.390733053605-0.02279174950290.1572235291090.01846533268790.04290509944530.2028506768350.04735766668660.1850684752960.3534108951430.0178633384482-0.02176747675220.3172802074770.04310459329220.25166728649127.743720537113.105083725132.56922431
46.74914872657-0.438237882993-4.631665606591.610959904570.452555424675.46129007051-0.166450828158-0.14141819874-0.0160873436520.08304365809990.0562277124751-0.1277224696310.1638048349960.06541153917170.1031834014790.330413577326-0.00250785346994-0.04526829434820.2960164416650.04317454543150.25994197976732.599703908112.793818997723.2236591842
50.959953709825-0.1147434084130.245890667660.67837678255-0.3287552033981.84931241662-0.04541444791690.0631079869283-0.0528848445831-0.05877535234830.008738960897080.02319333574540.205485788875-0.05940300041230.03328965774410.349989866361-0.01260909056230.01136590857590.28772532240.005166703976430.30941330842227.475989727912.478267978811.1076073534
62.61461219277-1.081766991982.463523250189.23246224055-2.514599469942.576339700680.0563637751668-0.227559773393-0.3770663772940.4519660122140.1094657871160.7021684904690.473127652768-1.12280528416-0.06227648198740.460256721751-0.2514451447910.0185297765270.6021925077820.05027508032770.444388892637.2580329251.3370216228914.0339240572
74.53872943646-1.75249567871-4.214765619313.104004792722.230317370794.07219710437-0.0620709299882-0.219799357095-0.156266404496-0.1908578833380.1176703910980.02339250951530.5058514886230.124122755884-0.07183289032620.393066705322-0.0346305004542-0.1023730229610.5447303402750.004208626607170.28704713585317.51068404426.45765159351-0.747728470032
80.964862177598-0.3264523292960.1647370045881.808197203780.2214693978533.658945385610.1340955853180.190990937659-0.104861194813-0.20964671903-0.1998195539570.2825371380410.235997815086-0.3151705711590.04429369810620.404371889119-0.00438971862974-0.06746577767760.480158513786-0.1230680067980.3884325643080.233688396791.83922612971-55.7143862352
95.24771710659-1.071447955521.458481287182.300382809460.0829111193832.083120576810.07074768056160.212412294646-0.161296265443-0.0848795863445-0.08049172075910.032591153060.136723190991-0.01963737398020.009927222725510.3761901047640.00399315163073-0.03206461041380.347467966298-0.08822103773850.2683444316617.533307533422.60157237363-48.5374932393
101.37347536255-0.408176733259-0.01656440135861.727889200550.4428405631372.467290047470.1507542199860.119019565897-0.06531158233120.0292484673755-0.0475510343239-0.1382115373620.205774545190.349254136505-0.1058504773630.3255002599770.0106196073456-0.0275950085670.368064320518-0.07109579723510.28635796028115.85956396514.73975366646-44.1761696131
111.57653954717-0.373177366310.7620293043561.78748373362-0.1242145338752.616213900080.149428625625-0.191077248276-0.1506015270640.258586218549-0.1226393324910.164585125370.448755048081-0.246815758647-0.03457016978840.454916147724-0.08867543203680.03808493036060.370070785431-0.08097979332670.3162847156784.552326857812.53933919515-26.4443241897
122.277492206951.201138814062.306694107839.43348781337-2.797210339639.65077260112-0.0424510861906-0.5060500163110.5238931874860.0901617624830.158827665340.908089287472-0.690714885488-0.704504232783-0.1139974842550.3710323034930.0468038471710.05653322861890.399819558296-0.1201572621150.404019276506-1.4382544377122.2041628291-28.3469783976
136.61230298151-0.0805274982075.289033504361.53373968705-0.5362018815984.407437574190.2414560532370.328305739553-0.03710408661010.150437056784-0.219238835079-0.04717927797550.1584071866370.4931856121750.01015529939380.51046192886-0.09040311047940.04552395224770.450834839117-0.0514978347470.27732219512813.087071354611.354967624-21.2447787111
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 45 )AA1 - 451 - 45
22chain 'A' and (resid 46 through 86 )AA46 - 8646 - 86
33chain 'A' and (resid 87 through 118 )AA87 - 11887 - 118
44chain 'A' and (resid 119 through 170 )AA119 - 170119 - 170
55chain 'A' and (resid 171 through 486 )AA171 - 486171 - 480
66chain 'A' and (resid 487 through 513 )AA487 - 513481 - 507
77chain 'A' and (resid 514 through 542 )AA514 - 542508 - 536
88chain 'B' and (resid 4 through 118 )BC4 - 1181 - 115
99chain 'B' and (resid 119 through 170 )BC119 - 170116 - 167
1010chain 'B' and (resid 171 through 341 )BC171 - 341168 - 332
1111chain 'B' and (resid 342 through 486 )BC342 - 486333 - 477
1212chain 'B' and (resid 487 through 513 )BC487 - 513478 - 504
1313chain 'B' and (resid 514 through 543 )BC514 - 543505 - 534

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