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- PDB-7aiw: Crystal structure of Torpedo Californica acetylcholinesterase in ... -

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Basic information

Entry
Database: PDB / ID: 7aiw
TitleCrystal structure of Torpedo Californica acetylcholinesterase in complex with (E)-10-[(3-Chloro-6,7,10,11-tetrahydro-9-methyl-7,11-methanocycloocta[b]quinolin-12-yl)amino]-N-(4-hydroxy-3-methoxybenzyl)-6-decenamide
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Torpedo Californica acetylcholinesterase / AD / alzheimer disease
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / choline metabolic process / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / extracellular space / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-8U5 / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCoquelle, N. / Colletier, J.P.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of a Potent Dual Inhibitor of Acetylcholinesterase and Butyrylcholinesterase with Antioxidant Activity that Alleviates Alzheimer-like Pathology in Old APP/PS1 Mice.
Authors: Viayna, E. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Cisternas, P. / Oliva, C.A. / Sanchez-Lopez, E. / Ettcheto, M. / Bartolini, M. / De Simone, A. / Ricchini, M. / Rendina, M. / Pons, M. / ...Authors: Viayna, E. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Cisternas, P. / Oliva, C.A. / Sanchez-Lopez, E. / Ettcheto, M. / Bartolini, M. / De Simone, A. / Ricchini, M. / Rendina, M. / Pons, M. / Firuzi, O. / Perez, B. / Saso, L. / Andrisano, V. / Nachon, F. / Brazzolotto, X. / Garcia, M.L. / Camins, A. / Silman, I. / Jean, L. / Inestrosa, N.C. / Colletier, J.P. / Renard, P.Y. / Munoz-Torrero, D.
History
DepositionSep 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)134,93115
Polymers131,9412
Non-polymers2,99013
Water17,871992
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,93115
Polymers131,9412
Non-polymers2,99013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_856-x+3,y+1/2,-z+3/21
Buried area3790 Å2
ΔGint-5 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.930, 106.510, 150.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 65970.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Tetronarce californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#3: 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.: 6 / 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 , 5 types, 999 molecules

#2: Chemical ChemComp-8U5 / E)-10-[(3-Chloro-6,7,10,11-tetrahydro-9-methyl-7,11-methanocycloocta[b]quinolin-12-yl)amino]-N-(4-hydroxy-3-methoxybenzyl)-6-decenamide


Mass: 592.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H46ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES 28-32% PEG 200 / PH range: 5.8-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 115995 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.21
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 11815 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xi4

2xi4


Resolution: 1.9→46.081 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 5701 5 %
Rwork0.1895 108262 -
obs0.1912 113963 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.94 Å2 / Biso mean: 32.3839 Å2 / Biso min: 16.44 Å2
Refinement stepCycle: final / Resolution: 1.9→46.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8456 0 197 992 9645
Biso mean--47.84 40.6 -
Num. residues----1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079076
X-RAY DIFFRACTIONf_angle_d0.97512346
X-RAY DIFFRACTIONf_chiral_restr0.1251293
X-RAY DIFFRACTIONf_plane_restr0.0061594
X-RAY DIFFRACTIONf_dihedral_angle_d14.5685418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.3681870.3502353897
1.9216-1.94420.37571890.3086357098
1.9442-1.96790.33361880.2961357598
1.9679-1.99280.3331900.2703360299
1.9928-2.0190.31761900.2601360298
2.019-2.04670.27151900.253361398
2.0467-2.07590.30061820.2524349396
2.0759-2.10690.26181900.2318360899
2.1069-2.13990.27811910.2218363299
2.1399-2.17490.27121920.2206364299
2.1749-2.21240.27991910.2228361699
2.2124-2.25270.26161880.2345356297
2.2527-2.2960.26741910.2039363099
2.296-2.34290.22061920.1996364499
2.3429-2.39380.21691900.1932361398
2.3938-2.44950.22911900.1862360498
2.4495-2.51070.23641920.1844364299
2.5107-2.57860.20421900.1933360698
2.5786-2.65450.25561890.1958359897
2.6545-2.74020.23421880.1891356497
2.7402-2.83810.23541890.1893360597
2.8381-2.95170.2211860.1908355796
2.9517-3.0860.24631900.1911360997
3.086-3.24870.23161900.1862361498
3.2487-3.45210.23091920.1816362797
3.4521-3.71860.18371910.1626363497
3.7186-4.09260.17751920.1513363497
4.0926-4.68430.16161940.141369098
4.6843-5.89980.17761930.156365296
5.8998-46.0810.19151940.1831368693

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