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

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Basic information

Entry
Database: PDB / ID: 7aix
TitleCrystal structure of Torpedo Californica acetylcholinesterase in complex with 2-{1-[4-(12-Amino-3-chloro-6,7,10,11-tetrahydro-7,11-methanocycloocta[b]quinolin-9-yl)butyl]-1H-1,2,3-triazol-4-yl}-N-[4-hydroxy-3-methoxybenzyl]acetamide
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-8U2 / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8085
Polymers65,9711
Non-polymers8374
Water7,746430
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,61510
Polymers131,9412
Non-polymers1,6748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area2640 Å2
ΔGint-22 kcal/mol
Surface area39140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.838, 112.838, 136.765
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1078-

HOH

21A-1093-

HOH

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 65970.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetronarce californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-8U2 / 2-{1-[4-(12-Amino-3-chloro-6,7,10,11-tetrahydro-7,11-methanocycloocta[b]quinolin-9-yl)butyl]-1H-1,2,3-triazol-4-yl}-N-[4-hydroxy-3-methoxybenzyl]acetamide


Mass: 589.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H37ClN6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 3.81 Å3/Da / Density % sol: 67.72 %
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: MASSIF-3 / Wavelength: 0.9679 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9679 Å / Relative weight: 1
ReflectionResolution: 1.86→46.012 Å / Num. obs: 83186 / % possible obs: 98 % / Redundancy: 3 % / Biso Wilson estimate: 43.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.9
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8635 / CC1/2: 0.77

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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: 1.86→46.012 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 4158 5 %
Rwork0.177 79019 -
obs0.178 83177 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.33 Å2 / Biso mean: 41.1619 Å2 / Biso min: 23.56 Å2
Refinement stepCycle: final / Resolution: 1.86→46.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 57 430 4727
Biso mean--46.84 49.35 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084506
X-RAY DIFFRACTIONf_angle_d0.8536133
X-RAY DIFFRACTIONf_chiral_restr0.052635
X-RAY DIFFRACTIONf_plane_restr0.005798
X-RAY DIFFRACTIONf_dihedral_angle_d14.7482693
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.86-1.88110.33051330.3342264598
1.8811-1.90330.36311230.3062257597
1.9033-1.92650.28371440.2769262698
1.9265-1.95090.29941520.2675261599
1.9509-1.97650.28131490.2672258398
1.9765-2.00360.27751330.2482259998
2.0036-2.03220.27361270.2358255197
2.0322-2.06260.22661410.222263598
2.0626-2.09480.22161130.222260998
2.0948-2.12920.25581110.2195267798
2.1292-2.16590.23521330.2186263099
2.1659-2.20530.21111480.2087259299
2.2053-2.24770.2261550.2264999
2.2477-2.29350.20631360.1914261699
2.2935-2.34340.22621340.1935263999
2.3434-2.39790.21051490.1858266699
2.3979-2.45790.21971350.1796262599
2.4579-2.52430.21531460.1851261899
2.5243-2.59860.20141490.1849262799
2.5986-2.68250.21741400.1859267899
2.6825-2.77830.22521340.1845261498
2.7783-2.88960.22171410.1789263799
2.8896-3.02110.20841450.1785265098
3.0211-3.18030.20711240.1799266098
3.1803-3.37950.20151460.1724262198
3.3795-3.64030.16741520.1625264198
3.6403-4.00650.18041360.1442262996
4.0065-4.58580.15191360.1396263597
4.5858-5.77580.15541540.1436266797
5.7758-46.0120.18241390.1855281097

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