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- PDB-1e3q: TORPEDO CALIFORNICA ACETYLCHOLINESTERASE COMPLEXED WITH BW284C51 -

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Basic information

Entry
Database: PDB / ID: 1e3q
TitleTORPEDO CALIFORNICA ACETYLCHOLINESTERASE COMPLEXED WITH BW284C51
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SERINE HYDROLASE / INHIBITOR
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / 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
Chem-EBW / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsFelder, C.E. / Harel, M. / Silman, I. / Sussman, J.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of a Complex of the Potent and Specific Inhibitor Bw284C51 with Torpedo Californica Acetylcholinesterase
Authors: Felder, C.E. / Harel, M. / Silman, I. / Sussman, J.L.
#1: Journal: Structure / Year: 1999
Title: Structure of Acetylcholinesterase Complexed with E2020 (Aricept): Implications for the Design of New Anti-Alzheimer Drugs
Authors: Kryger, G. / Silman, I. / Sussman, J.L.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase
Authors: Harel, M. / Schalk, I. / Ehret-Sabattier, L. / Bouet, F. / Goeldner, M. / Hirth, C. / Axelsen, P.H. / Silman, I. / Sussman, J.L.
History
DepositionJun 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2000Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Jul 12, 2017Group: Advisory / Category: database_PDB_caveat / Item: _database_PDB_caveat.text
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4916
Polymers61,3251
Non-polymers1,1665
Water2,306128
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,98312
Polymers122,6502
Non-polymers2,33310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3560 Å2
ΔGint-29.6 kcal/mol
Surface area41230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.000, 114.000, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE ENZYME IS A GPI-ANCHORED DIMER. THE TWO MONOMERS IN THE DIMER ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLDSYMMETRY.

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Components

#1: Protein ACETYLCHOLINESTERASE


Mass: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray)
Organ: ELECTRIC ORGAN / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-EBW / 4-(5-{4-[DIMETHYL(PROP-2-ENYL)AMMONIO]PHENYL}-3-OXOPENTYL)-N,N-DIMETHYL-N-PROP-2-ENYLBENZENAMINIUM


Mass: 406.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growpH: 5.8 / Details: pH 5.80
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Sussman, J.L., (1991) Science, 253, 872.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
261 %satammonium sulfate1reservoir
3360 mMNa,K-phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MULTIWIRE XENTRONICS / Detector: AREA DETECTOR / Date: Dec 15, 1991 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.83→30 Å / Num. obs: 48244 / % possible obs: 77.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.9 Å2 / Rsym value: 0.104
Reflection shellResolution: 2.83→3.16 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.286 / % possible all: 47
Reflection
*PLUS
Num. obs: 22837 / Num. measured all: 36141 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 47 % / Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Resolution: 2.85→18.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 8544140.69 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE ASP 1, ASP 2 AND THE C-TERMINAL RESIDUES AFTER THR 535.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1110 4.9 %RANDOM
Rwork0.19 ---
obs0.19 22783 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.655 Å2 / ksol: 0.329151 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å211.37 Å20 Å2
2--4.21 Å20 Å2
3----8.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a1.02 Å0.9 Å
Refinement stepCycle: LAST / Resolution: 2.85→18.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 77 128 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.262.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 114 5.1 %
Rwork0.386 2117 -
obs--55.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BW.PARCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMBW.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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