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- PDB-5fum: Mus musculus acetylcholinesterase in complex with AL200 -

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Basic information

Entry
Database: PDB / ID: 5fum
TitleMus musculus acetylcholinesterase in complex with AL200
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / VECTOR CONTROL / INSECTICIDE / SELECTIVE / MALARIA / DENGUE
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 / 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 / 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, catalytic domain ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SOF / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsKnutsson, S. / Engdahl, C. / Ekstrom, F. / Linusson, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of Selective Inhibitors Targeting Acetylcholinesterase 1 from Disease-Transmitting Mosquitoes.
Authors: Engdahl, C. / Knutsson, S. / Ekstrom, F.J. / Linusson, A.
History
DepositionJan 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)122,23810
Polymers120,4682
Non-polymers1,7708
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-11.5 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.660, 110.757, 227.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ACETYLCHOLINESTERASE /


Mass: 60233.984 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#2: Chemical ChemComp-SOF / 2-(biphenyl-4-yloxy)-1-[4-(4-ethylpiperazin-1-yl)piperidin-1-yl]ethanone


Mass: 407.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33N3O2
#3: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


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


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 4.11 Å3/Da / Density % sol: 70.1 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.034
DetectorDetector: CCD / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034 Å / Relative weight: 1
ReflectionResolution: 2.5→29.08 Å / Num. obs: 69320 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.69
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.584 / Mean I/σ(I) obs: 2.35 / % possible all: 99.28

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→29.076 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 28.66 / Stereochemistry target values: ML / Details: PH 7
RfactorNum. reflection% reflection
Rfree0.2265 1387 2 %
Rwork0.1958 --
obs0.1965 69061 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8327 0 123 129 8579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048730
X-RAY DIFFRACTIONf_angle_d0.89211899
X-RAY DIFFRACTIONf_dihedral_angle_d17.2263204
X-RAY DIFFRACTIONf_chiral_restr0.0321268
X-RAY DIFFRACTIONf_plane_restr0.0041558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.39171450.31116602X-RAY DIFFRACTION99
2.5893-2.69290.31511500.2816642X-RAY DIFFRACTION99
2.6929-2.81540.34331320.26756676X-RAY DIFFRACTION99
2.8154-2.96370.32211390.2686672X-RAY DIFFRACTION99
2.9637-3.14920.29931520.24856712X-RAY DIFFRACTION99
3.1492-3.3920.25011150.23266770X-RAY DIFFRACTION100
3.392-3.73270.23361490.19356779X-RAY DIFFRACTION100
3.7327-4.27140.17751320.16816823X-RAY DIFFRACTION100
4.2714-5.37590.17091320.15066878X-RAY DIFFRACTION100
5.3759-29.07830.18111410.16537120X-RAY DIFFRACTION99

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