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- PDB-2whr: Crystal structure of acetylcholinesterase in complex with K027 -

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Basic information

Entry
Database: PDB / ID: 2whr
TitleCrystal structure of acetylcholinesterase in complex with K027
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SERINE ESTERASE / ALTERNATIVE SPLICING / NEUROTRANSMITTER DEGRADATION / K026 / OXIME / SYNAPSE / MEMBRANE / SECRETED / CELL MEMBRANE / DISULFIDE BOND / CHOLINESTERASE / GPI-ANCHOR / LIPOPROTEIN / GLYCOPROTEIN / CELL JUNCTION
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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 ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / 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
BROMIDE ION / CARBONATE ION / Chem-K27 / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å
AuthorsEkstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.-G. / Schneider, G. / Pang, Y.-P.
CitationJournal: Plos One / Year: 2009
Title: Structure of Hi-6Sarin-Acetylcholinesterase Determined by X-Ray Crystallography and Molecular Dynamics Simulation: Reactivator Mechanism and Design.
Authors: Ekstrom, F. / Hornberg, A. / Artursson, E. / Hammarstrom, L.-G. / Schneider, G. / Pang, Y.-P.
History
DepositionMay 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,71015
Polymers120,4682
Non-polymers2,24213
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint30 kcal/mol
Surface area37180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.320, 111.410, 226.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60233.984 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1
Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
Production host: HOMO SAPIENS (human) / References: UniProt: P21836, acetylcholinesterase
#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

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Non-polymers , 7 types, 671 molecules

#2: Chemical ChemComp-K27 / 4-carbamoyl-1-(3-{4-[(E)-(hydroxyimino)methyl]pyridinium-1-yl}propyl)pyridinium


Mass: 286.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N4O2
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O3
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7 / Details: 26-30 % (V/V) PEG750MME, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.131
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.131 Å / Relative weight: 1
ReflectionResolution: 2.6→19.8 Å / Num. obs: 64776 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 43.21 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.1
Reflection shellResolution: 2.54→2.7 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 7.2 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.545→19.809 Å / SU ML: 0.33 / σ(F): 1.41 / Phase error: 19 / Stereochemistry target values: ML / Details: RESIDUES 258-264 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2192 1292 2 %
Rwork0.1698 --
obs0.1708 64699 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.554 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1488 Å20 Å20 Å2
2--0.2844 Å20 Å2
3----0.1355 Å2
Refinement stepCycle: LAST / Resolution: 2.545→19.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 143 660 9139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048748
X-RAY DIFFRACTIONf_angle_d0.92111916
X-RAY DIFFRACTIONf_dihedral_angle_d18.3493132
X-RAY DIFFRACTIONf_chiral_restr0.0631274
X-RAY DIFFRACTIONf_plane_restr0.0041564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5449-2.64650.27041370.21385949X-RAY DIFFRACTION85
2.6465-2.76670.26611480.19237083X-RAY DIFFRACTION100
2.7667-2.91210.25441430.18267105X-RAY DIFFRACTION100
2.9121-3.09390.20861570.17687094X-RAY DIFFRACTION100
3.0939-3.33180.23441370.16797118X-RAY DIFFRACTION100
3.3318-3.66520.18831410.16027128X-RAY DIFFRACTION100
3.6652-4.19110.21121390.13817187X-RAY DIFFRACTION100
4.1911-5.26390.16691440.13787259X-RAY DIFFRACTION100
5.2639-19.80990.21481460.17297484X-RAY DIFFRACTION100

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