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- PDB-6fsd: Mus musculus acetylcholinesterase in complex with 2-(4-Biphenylyl... -

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Basic information

Entry
Database: PDB / ID: 6fsd
TitleMus musculus acetylcholinesterase in complex with 2-(4-Biphenylyloxy)-N-[3-(1-piperidinyl)propyl]-acetamide hydrochloride (10)
ComponentsAcetylcholinesterase
KeywordsPROTEIN BINDING / Inhibitor / hydrolase / acetylcholinesterase
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / 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 ...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-1PG / Chem-E5H / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsKnutsson, S. / Engdahl, C. / Kumari, R. / Kindahl, T. / Forsgren, N. / Lindgren, C. / Kitur, S. / Kamau, L. / Ekstrom, F. / Linusson, A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2014-4218 Sweden
Swedish Research Council2014-2636 Sweden
CitationJournal: J.Med.Chem. / Year: 2018
Title: Noncovalent Inhibitors of Mosquito Acetylcholinesterase 1 with Resistance-Breaking Potency.
Authors: Knutsson, S. / Engdahl, C. / Kumari, R. / Forsgren, N. / Lindgren, C. / Kindahl, T. / Kitur, S. / Wachira, L. / Kamau, L. / Ekstrom, F. / Linusson, A.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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

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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)121,6868
Polymers120,3242
Non-polymers1,3626
Water2,972165
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint7 kcal/mol
Surface area37040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.013, 110.327, 227.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 60161.922 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 cells / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-E5H / 2-(4-phenylphenoxy)-~{N}-(3-piperidin-1-ylpropyl)ethanamide


Mass: 352.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: PEG 750, Hepes / PH range: 6.8-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→39.58 Å / Num. obs: 51940 / % possible obs: 95 % / Redundancy: 5.6 % / Biso Wilson estimate: 47.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07983 / Rrim(I) all: 0.08736 / Net I/σ(I): 18.22
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.5594 / Mean I/σ(I) obs: 4.02 / Num. unique obs: 5210 / CC1/2: 0.957 / Rrim(I) all: 0.6129 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
Coot0.7.2 (revision 4730)model building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.7→39.578 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48
RfactorNum. reflection% reflection
Rfree0.2342 1035 1.99 %
Rwork0.1906 --
obs0.1915 51940 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 86 165 8587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098672
X-RAY DIFFRACTIONf_angle_d1.03711830
X-RAY DIFFRACTIONf_dihedral_angle_d17.1375107
X-RAY DIFFRACTIONf_chiral_restr0.0581264
X-RAY DIFFRACTIONf_plane_restr0.0071550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84230.35241470.27557289X-RAY DIFFRACTION97
2.8423-3.02030.32631550.257272X-RAY DIFFRACTION96
3.0203-3.25340.31471580.24347275X-RAY DIFFRACTION96
3.2534-3.58060.27841360.20617293X-RAY DIFFRACTION96
3.5806-4.09830.22421470.1787247X-RAY DIFFRACTION95
4.0983-5.16160.16541420.15197239X-RAY DIFFRACTION94
5.1616-39.58180.18961500.16867288X-RAY DIFFRACTION91

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