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- PDB-1w4l: Complex of TcAChE with bis-acting galanthamine derivative -

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Basic information

Entry
Database: PDB / ID: 1w4l
TitleComplex of TcAChE with bis-acting galanthamine derivative
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ALZHEIMER'S DISEASE / CHOLINESTERASE / GLYCOPROTEIN / GPI-ANCHOR / MUSCLE / NERVE / NEUROTRANSMITTER DEGRADATION / SERINE ESTERASE / SERINE HYDROLASE / SYNAPSE
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, 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 ...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 DERIVATIVE / Acetylcholinesterase
Similarity search - Component
Biological speciesTORPEDO CALIFORNICA (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.16 Å
AuthorsGreenblatt, H.M. / Guillou, C. / Guenard, D. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2004
Title: The complex of a bivalent derivative of galanthamine with torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design.
Authors: Greenblatt, H.M. / Guillou, C. / Guenard, D. / Argaman, A. / Botti, S. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L.
#1: 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.
History
DepositionJul 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
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)62,7225
Polymers61,3251
Non-polymers1,3964
Water5,567309
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,44310
Polymers122,6502
Non-polymers2,7938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)111.327, 111.327, 136.859
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: 61325.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) TORPEDO CALIFORNICA (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: Chemical ChemComp-GL8 / GALANTHAMINE DERIVATIVE / (4AR,6S,8AR)-11-[8-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)OCTYL]-6-HYDROXY-3-METHOXY-5,6,9,10-TETRAHYDRO-4AH-[1]BENZOFURO[3A,3,2-EF][2]BENZAZEPIN-11-IUM


Mass: 529.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H37N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST THREE N-TERMINAL RESIDUES AND LAST 8 C-TERMINAL RESIDUES NOT SEEN IN DENSITY, AND NOT ...FIRST THREE N-TERMINAL RESIDUES AND LAST 8 C-TERMINAL RESIDUES NOT SEEN IN DENSITY, AND NOT INCLUDED IN COORDINATE FILE. RESIDUES 486-489 HAVE POOR DENSITY, AND ARE NOT MODELED.

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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: 4.3 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 277 K / pH: 5.5
Details: PROTEIN WAS CRYSTALLISED FROM 35-40% W/V PEG 200 0.1M MES PH 5.8 4 DEG. CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.16→40 Å / Num. obs: 52750 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.16→39.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2157149.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2636 5 %RANDOM
Rwork0.184 ---
obs0.184 52748 98.6 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 57.5284 Å2 / ksol: 0.381833 e/Å3
Displacement parametersBiso mean: 32.91 Å2
Baniso -1Baniso -2Baniso -3
1-7.31 Å25.71 Å20 Å2
2--7.31 Å20 Å2
3----14.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.16→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 95 309 4608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.932
X-RAY DIFFRACTIONc_scangle_it3.892.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 255 5 %
Rwork0.204 4844 -
obs--53.8 %

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