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- PDB-4w63: TORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH A TACRIN... -

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Basic information

Entry
Database: PDB / ID: 4w63
TitleTORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH A TACRINE-BENZOFURAN HYBRID INHIBITOR
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / multitarget drug / enzyme-inhibitor complex / tacrine / benzofuran
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / choline metabolic process / 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
Chem-HTB / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPesaresi, A. / Samez, S. / Lamba, D.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Novel Tacrine-Benzofuran Hybrids as Potent Multitarget-Directed Ligands for the Treatment of Alzheimer's Disease: Design, Synthesis, Biological Evaluation, and X-ray Crystallography.
Authors: Zha, X. / Lamba, D. / Zhang, L. / Lou, Y. / Xu, C. / Kang, D. / Chen, L. / Xu, Y. / Zhang, L. / De Simone, A. / Samez, S. / Pesaresi, A. / Stojan, J. / Lopez, M.G. / Egea, J. / Andrisano, V. / Bartolini, M.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Advisory / Data collection / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_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 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)61,7565
Polymers60,4471
Non-polymers1,3084
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint10 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.220, 112.220, 138.720
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: 60447.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
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: obtained synthetically
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: obtained synthetically / 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-HTB / N-(1-benzofuran-2-ylmethyl)-N'-(1,2,3,4-tetrahydroacridin-9-yl)heptane-1,7-diamine


Mass: 441.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H35N3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 30% PRG200, 100mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.22 Å / Num. obs: 22808 / % possible obs: 90 % / Redundancy: 5 % / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.4 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLM7.0.7data reduction
SCALA3.3.2.1data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA5

1ea5


Resolution: 2.8→45.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.52 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.6 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1132 5 %RANDOM
Rwork0.192 ---
obs0.195 21631 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å21.17 Å20 Å2
2--1.17 Å20 Å2
3----3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 89 95 4447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194460
X-RAY DIFFRACTIONr_bond_other_d0.0030.024070
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.9676067
X-RAY DIFFRACTIONr_angle_other_deg0.9523.0049333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.325533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31923.971209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48215683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9211524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021081
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5165.8152135
X-RAY DIFFRACTIONr_mcbond_other4.5155.8132134
X-RAY DIFFRACTIONr_mcangle_it6.7528.7192667
X-RAY DIFFRACTIONr_mcangle_other6.7528.7212668
X-RAY DIFFRACTIONr_scbond_it4.4926.1682325
X-RAY DIFFRACTIONr_scbond_other4.4916.1672326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9449.133401
X-RAY DIFFRACTIONr_long_range_B_refined9.70547.2665357
X-RAY DIFFRACTIONr_long_range_B_other9.70447.2685355
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 63 -
Rwork0.356 1630 -
obs--90.68 %

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