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- PDB-1qti: Acetylcholinesterase (E.C.3.1.1.7) -

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Basic information

Entry
Database: PDB / ID: 1qti
TitleAcetylcholinesterase (E.C.3.1.1.7)
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ALZHEIMER'S DISEASE / DRUG / SERINE HYDROLASE / ALPHA/BETA HYDROLASE / NEUROTRANSMITTER CLEAVEAGE / CATALYTIC TRIAD
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
(-)-GALANTHAMINE / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsBartolucci, C. / Perola, E. / Pilger, C. / Fels, G. / Lamba, D.
Citation
Journal: Proteins / Year: 2001
Title: Three-dimensional structure of a complex of galanthamine (Nivalin) with acetylcholinesterase from Torpedo californica: implications for the design of new anti-Alzheimer drugs
Authors: Bartolucci, C. / Perola, E. / Pilger, C. / Fels, G. / Lamba, D.
#1: Journal: Science / Year: 1991
Title: Atomic Structure of Acetylcholinesterase from Torpedo californica: A Prototypic Acetylcholine-Binding Protein
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I.
#2: Journal: Bioorg.Med.Chem. / Year: 1998
Title: Potent Acetylcholinesterase Inhibitors-Design, Synthesis, and Structure- Activity Relationships of Bis-Interacting Ligands in the Galanthamine Series
Authors: Mary, A. / Renko, D.Z. / Guillou, C. / Thal, C.
#3: Journal: Tetrahedron Lett. / Year: 1998
Title: New Kilogram-Synthesis of the Anti-Alzheimer Drug (-)-Galanthamine
Authors: Czollner, L. / Frantsits, W. / Kuenburg, B. / Hedenig, U. / Frohlich, J. / Jordis, U.
#4: Journal: To be Published
Title: Prediction of the Binding Site of (-)-Galanthamine in Acetylcholinesterase by Docking Studies
Authors: Pilger, C. / Bartolucci, C. / Lamba, D. / Tropsha, A. / Fels, G.
History
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 2, 2021Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_prop ...pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_biol / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)61,0242
Polymers60,7371
Non-polymers2871
Water3,099172
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0484
Polymers121,4732
Non-polymers5752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3230 Å2
ΔGint-10 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.824, 110.824, 136.445
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 /


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPLEXED WITH GALANTHAMINE
Source: (natural) Torpedo californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-GNT / (-)-GALANTHAMINE / Galantamine


Mass: 287.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21NO3 / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.98 Å3/Da / Density % sol: 69.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 40% PEG 200, 100MM MES (pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 6 / Details: Sussman, J.L., (1988) J. Mol. Biol., 203, 821.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 %PEG2001reservoir
28-10 mg/mlprotein1drop
318 %PEG2001drop
40.5 MMES1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 42574 / Num. obs: 38494 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.21 / % possible all: 85.9
Reflection
*PLUS
Num. obs: 42574 / Observed criterion σ(I): 0 / Num. measured all: 188745
Reflection shell
*PLUS
% possible obs: 85.9 % / Num. unique obs: 5493 / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.5→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: IN THE LAST FEW REFINEMENT CYCLES VERY WEAK REFLECTIONS WITH A RATIO FCALC/FOBS GREATER THAN 2.5, CLEARLY AFFECTED BY SYSTEMATIC MEASUREMENTS ERRORS, WERE EXCLUDED FROM THE CALCULATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1332 4.9 %RANDOM
Rwork0.192 ---
obs0.192 27322 80.4 %-
all-32390 --
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 21 172 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.61.5
X-RAY DIFFRACTIONx_mcangle_it3.892
X-RAY DIFFRACTIONx_scbond_it42
X-RAY DIFFRACTIONx_scangle_it5.512.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 213 5.1 %
Rwork0.269 4023 -
obs--81.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.64
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.269

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