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

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Basic information

Entry
Database: PDB / ID: 7ait
TitleCrystal structure of Torpedo Californica acetylcholinesterase in complex with 7-[(3-Chloro-6,7,10,11-tetrahydro-9-methyl-7,11-methanocycloocta[b]quinolin-12-yl)amino]-N-(4-hydroxy-3-methoxybenzyl)heptanamide
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-8UK / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Oct 16, 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)133,0384
Polymers131,9412
Non-polymers1,0962
Water13,151730
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0384
Polymers131,9412
Non-polymers1,0962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1880 Å2
ΔGint-11 kcal/mol
Surface area38630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.420, 106.850, 151.510
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-8UK / 7-[(3-Chloro-6,7,10,11-tetrahydro-9-methyl-7,11-methanocycloocta[b]quinolin-12-yl)amino]-N-(4-hydroxy-3-methoxybenzyl)heptanamide


Mass: 548.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H38ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 730 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 28-32% PEG 200 50mM MES / 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: MASSIF-1 / Wavelength: 0.9801 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: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 87818 / % possible obs: 99.7 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6450 / CC1/2: 0.916

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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: 2.1→46.21 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 4185 4.77 %
Rwork0.1892 83518 -
obs0.191 87703 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.09 Å2 / Biso mean: 35.3786 Å2 / Biso min: 18.69 Å2
Refinement stepCycle: final / Resolution: 2.1→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8474 0 78 730 9282
Biso mean--40.4 41.27 -
Num. residues----1064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088920
X-RAY DIFFRACTIONf_angle_d0.90412142
X-RAY DIFFRACTIONf_chiral_restr0.0541262
X-RAY DIFFRACTIONf_plane_restr0.0061580
X-RAY DIFFRACTIONf_dihedral_angle_d12.415314
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12390.33391430.25472711100
2.1239-2.14890.29781460.2406275899
2.1489-2.17510.30171440.23882755100
2.1751-2.20260.31591470.24752783100
2.2026-2.23160.36371390.3047264297
2.2316-2.26220.45571440.40162744100
2.2622-2.29450.31011400.2823265796
2.2945-2.32870.25811260.22142781100
2.3287-2.36510.29341380.20482780100
2.3651-2.40390.24011400.19232748100
2.4039-2.44530.26161230.19182776100
2.4453-2.48980.23121460.18842773100
2.4898-2.53770.23541400.17782742100
2.5377-2.58950.22311360.18222790100
2.5895-2.64580.22691380.17972790100
2.6458-2.70730.22181340.18462765100
2.7073-2.7750.24181450.18442778100
2.775-2.850.22921580.18532760100
2.85-2.93390.21731600.18592753100
2.9339-3.02860.2161450.19242781100
3.0286-3.13680.25931370.19432807100
3.1368-3.26240.21811600.18592764100
3.2624-3.41080.2121280.18872823100
3.4108-3.59050.21091430.17582797100
3.5905-3.81540.2413730.17872882100
3.8154-4.10980.18521480.15712804100
4.1098-4.52310.16621270.14592847100
4.5231-5.17680.16671380.14412856100
5.1768-6.51940.2031510.17262869100
6.5194-46.210.1961480.1948300299

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