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- PDB-6g1w: Crystal structure of Torpedo Californica acetylcholinesterase in ... -

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Basic information

Entry
Database: PDB / ID: 6g1w
TitleCrystal structure of Torpedo Californica acetylcholinesterase in complex with 2-{1-[2-(6-Chloro-1,2,3,4-tetrahydroacridin-9-ylamino)ethyl]-1H-1,2,3-triazol-4-yl}-N-[4-(hydroxy)-3-methoxybenzyl]acetamide
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Torpedo Californica acetylcholinesterase / AD / alzheimer disease
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-E0Z / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCoquelle, N. / Colletier, J.P.
CitationJournal: Molecules / Year: 2018
Title: Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis.
Authors: Galdeano, C. / Coquelle, N. / Cieslikiewicz-Bouet, M. / Bartolini, M. / Perez, B. / Clos, M.V. / Silman, I. / Jean, L. / Colletier, J.P. / Renard, P.Y. / Munoz-Torrero, D.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionApr 4, 2018ID: 6FOV
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 2.0May 1, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Jul 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
Revision 2.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,06615
Polymers127,5282
Non-polymers2,53813
Water16,448913
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-35 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.820, 106.810, 151.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 63763.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Tetronarce californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#2: 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.: 6
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
#3: Chemical ChemComp-E0Z / 2-[1-[2-[(3-chloranylacridin-9-yl)amino]ethyl]-1,2,3-triazol-4-yl]-~{N}-[(3-methoxy-4-oxidanyl-phenyl)methyl]ethanamide


Mass: 516.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H25ClN6O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 30% PEG 200/50 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→45.7 Å / Num. obs: 117742 / % possible obs: 99.71 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.286 / Mean I/σ(I) obs: 1 / Num. unique obs: 11618 / CC1/2: 0.588 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xi4

2xi4


Resolution: 1.9→45.7 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.92
RfactorNum. reflection% reflection
Rfree0.2177 5876 5 %
Rwork0.1882 --
obs0.1896 117504 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8450 0 163 913 9526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079007
X-RAY DIFFRACTIONf_angle_d0.84612262
X-RAY DIFFRACTIONf_dihedral_angle_d12.975308
X-RAY DIFFRACTIONf_chiral_restr0.0531286
X-RAY DIFFRACTIONf_plane_restr0.0051588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.37421930.36453640X-RAY DIFFRACTION99
1.9216-1.94420.33711940.33623679X-RAY DIFFRACTION100
1.9442-1.96790.31591930.30953690X-RAY DIFFRACTION100
1.9679-1.99280.34341940.30163681X-RAY DIFFRACTION100
1.9928-2.01910.35311930.2793656X-RAY DIFFRACTION100
2.0191-2.04670.30211910.26243696X-RAY DIFFRACTION100
2.0467-2.0760.28341950.24653681X-RAY DIFFRACTION100
2.076-2.1070.2761930.22453681X-RAY DIFFRACTION100
2.107-2.13990.24851940.22813709X-RAY DIFFRACTION100
2.1399-2.1750.26461930.21793671X-RAY DIFFRACTION100
2.175-2.21250.26911940.22033682X-RAY DIFFRACTION100
2.2125-2.25270.26771940.21123684X-RAY DIFFRACTION100
2.2527-2.2960.23351930.20073710X-RAY DIFFRACTION100
2.296-2.34290.25051940.18833669X-RAY DIFFRACTION100
2.3429-2.39380.21781960.1833712X-RAY DIFFRACTION100
2.3938-2.44950.22351940.18313688X-RAY DIFFRACTION100
2.4495-2.51080.24651970.18223724X-RAY DIFFRACTION100
2.5108-2.57860.22231950.18473706X-RAY DIFFRACTION100
2.5786-2.65450.20921970.18413736X-RAY DIFFRACTION100
2.6545-2.74020.20541950.1843701X-RAY DIFFRACTION100
2.7402-2.83810.21631970.18613735X-RAY DIFFRACTION100
2.8381-2.95170.23261960.19353724X-RAY DIFFRACTION100
2.9517-3.0860.24061970.19473726X-RAY DIFFRACTION100
3.086-3.24870.22131970.18913745X-RAY DIFFRACTION100
3.2487-3.45220.22531980.18793755X-RAY DIFFRACTION100
3.4522-3.71860.17881970.17033741X-RAY DIFFRACTION100
3.7186-4.09260.17142000.14993787X-RAY DIFFRACTION100
4.0926-4.68440.15512000.13873801X-RAY DIFFRACTION100
4.6844-5.89990.1692020.15243844X-RAY DIFFRACTION100
5.8999-46.1780.21282100.19113974X-RAY DIFFRACTION99

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