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- PDB-6eue: Rivastigmine analogue bound to Tc ACHE. -

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Basic information

Entry
Database: PDB / ID: 6eue
TitleRivastigmine analogue bound to Tc ACHE.
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Cholinesterase / alzheimer disease / organophosphate / carbamylated
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / 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 ...Acetylcholinesterase, fish/snake / 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
Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDe la Mora, E. / Brazzolotto, X. / Dighe, S.N. / Silman, I. / Weik, M. / Ross, B.
CitationJournal: Commun Chem / Year: 2019
Title: Rivastigmine and metabolite analogues with putative Alzheimer's disease-modifying properties in a Caenorhabditis elegans model
Authors: Dighe, S.N. / De la Mora, E. / Chan, S. / Kantham, S. / McColl, G. / Veliyat, S.K. / Miles, J.A. / McGeary, R.P. / Silman, I. / Weik, M. / Parat, M.P. / Brazzolotto, X. / Ross, B.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)62,0518
Polymers60,4171
Non-polymers1,6347
Water7,008389
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,10216
Polymers120,8342
Non-polymers3,26814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_767-x+2,-x+y+1,-z+7/31
Buried area5420 Å2
ΔGint8 kcal/mol
Surface area39310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.000, 112.000, 137.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 60417.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Tc AChE with carbamylated Ser200
Source: (natural) Tetronarce californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / AChE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6 / Details: Tc AChE with carbamylated Ser200
Source: (natural) Tetronarce californica (Pacific electric ray)
References: acetylcholinesterase
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5 / Details: MES 100 mM pH 5.5 PEG 200 32%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→39.6 Å / Num. obs: 67469 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.4 % / Biso Wilson estimate: 37.82 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.52
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.89 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.6 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.17
RfactorNum. reflection% reflection
Rfree0.225 3508 5.21 %
Rwork0.196 --
obs0.197 67375 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4245 0 66 389 4700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114547
X-RAY DIFFRACTIONf_angle_d1.9716177
X-RAY DIFFRACTIONf_dihedral_angle_d19.0941696
X-RAY DIFFRACTIONf_chiral_restr0.12645
X-RAY DIFFRACTIONf_plane_restr0.008803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02740.371170.372552X-RAY DIFFRACTION100
2.0274-2.05640.36841340.38022474X-RAY DIFFRACTION99
2.0564-2.08710.37141490.35682543X-RAY DIFFRACTION99
2.0871-2.11970.33841280.33832512X-RAY DIFFRACTION100
2.1197-2.15440.36181560.31432523X-RAY DIFFRACTION99
2.1544-2.19160.3321190.3142527X-RAY DIFFRACTION99
2.1916-2.23140.32991250.29392533X-RAY DIFFRACTION100
2.2314-2.27430.3521230.27282548X-RAY DIFFRACTION99
2.2743-2.32070.26481280.26292546X-RAY DIFFRACTION99
2.3207-2.37120.27531610.25942497X-RAY DIFFRACTION100
2.3712-2.42630.25991130.23772575X-RAY DIFFRACTION100
2.4263-2.4870.29011790.23822509X-RAY DIFFRACTION100
2.487-2.55420.31490.22662541X-RAY DIFFRACTION100
2.5542-2.62940.26221330.21152533X-RAY DIFFRACTION100
2.6294-2.71420.27341540.20482511X-RAY DIFFRACTION100
2.7142-2.81120.24321630.19332563X-RAY DIFFRACTION100
2.8112-2.92370.22621430.18492545X-RAY DIFFRACTION100
2.9237-3.05680.21531540.19532556X-RAY DIFFRACTION100
3.0568-3.21790.26151420.19992546X-RAY DIFFRACTION100
3.2179-3.41940.2251320.18132583X-RAY DIFFRACTION100
3.4194-3.68320.19011560.16562559X-RAY DIFFRACTION100
3.6832-4.05350.17661260.14892607X-RAY DIFFRACTION100
4.0535-4.63930.1531330.13752618X-RAY DIFFRACTION100
4.6393-5.8420.16751540.15042620X-RAY DIFFRACTION100
5.842-39.590.19281370.18432746X-RAY DIFFRACTION100

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