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

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Basic information

Entry
Database: PDB / ID: 7aiv
TitleCrystal structure of Torpedo Californica acetylcholinesterase in complex with 4-{[(3-Chloro-6,7,10,11-tetrahydro-9-methyl-7,11-methanocycloocta[b]quinolin-12-yl)amino]methyl}-N-(4-hydroxy-3-methoxybenzyl)benzamide
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-8UE / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 6, 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

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5103
Polymers131,9412
Non-polymers5681
Water4,342241
1
A: Acetylcholinesterase

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5103
Polymers131,9412
Non-polymers5681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_746-x+2,y-1/2,-z+3/21
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area38820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.030, 106.660, 151.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 568.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.34 %
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: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 48442 / % possible obs: 98.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.1
Reflection shellResolution: 2.55→2.62 Å / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.9 / 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: 2.55→19.984 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 2287 4.73 %
Rwork0.2079 46092 -
obs0.2104 48379 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.68 Å2 / Biso mean: 38.0157 Å2 / Biso min: 14.11 Å2
Refinement stepCycle: final / Resolution: 2.55→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8474 0 41 241 8756
Biso mean--45.71 38.21 -
Num. residues----1064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068880
X-RAY DIFFRACTIONf_angle_d0.83812088
X-RAY DIFFRACTIONf_chiral_restr0.0511260
X-RAY DIFFRACTIONf_plane_restr0.0051577
X-RAY DIFFRACTIONf_dihedral_angle_d13.5815276
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5501-2.60540.33761460.2745283898
2.6054-2.66590.31631350.2619287399
2.6659-2.73240.30451430.2555283299
2.7324-2.8060.32651490.2425286198
2.806-2.88840.30361610.233277498
2.8884-2.98130.29771490.2348287199
2.9813-3.08750.32541440.2497283998
3.0875-3.21060.33061540.2299281598
3.2106-3.35610.28751480.2343289199
3.3561-3.53210.27151520.2124290299
3.5321-3.75210.3095720.2402291598
3.7521-4.03960.24881590.1841290499
4.0396-4.44210.19381110.1646295899
4.4421-5.07560.20541660.155289798
5.0756-6.36030.23091450.1754291498
6.3603-19.9840.20741530.1955300897

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