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- PDB-6o4w: Binary complex of native hAChE with Donepezil -

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Basic information

Entry
Database: PDB / ID: 6o4w
TitleBinary complex of native hAChE with Donepezil
ComponentsAcetylcholinesterase
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / retina development in camera-type eye / cell adhesion / hydrolase activity / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleus / membrane / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / 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-E20 / NITRATE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGerlits, O. / Kovalevsky, A. / Radic, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1U01NS083451 United States
CitationJournal: Chem.Biol.Interact. / Year: 2019
Title: A new crystal form of human acetylcholinesterase for exploratory room-temperature crystallography studies.
Authors: Gerlits, O. / Ho, K.Y. / Cheng, X. / Blumenthal, D. / Taylor, P. / Kovalevsky, A. / Radic, Z.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value
Revision 1.4Oct 11, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)122,13614
Polymers120,5762
Non-polymers1,56012
Water6,666370
1
B: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,13614
Polymers120,5762
Non-polymers1,56012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z+1/31
Buried area5780 Å2
ΔGint-14 kcal/mol
Surface area37630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.792, 123.792, 129.413
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60287.977 Da / Num. of mol.: 2 / Fragment: residues 32-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-E20 / 1-BENZYL-4-[(5,6-DIMETHOXY-1-INDANON-2-YL)METHYL]PIPERIDINE / E2020


Mass: 379.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29NO3
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.82 Å3/Da / Density % sol: 74.46 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 10 mM sodium citrate, 100 mM HEPES, pH 7, and 6-8 % PEG6000 or PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 66738 / % possible obs: 92.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.5
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.425 / Num. unique obs: 8521

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.35→38.669 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.212 1978 2.41 %
Rwork0.1862 --
obs0.1868 81980 88.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→38.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 108 370 8854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038744
X-RAY DIFFRACTIONf_angle_d0.65511946
X-RAY DIFFRACTIONf_dihedral_angle_d14.9715092
X-RAY DIFFRACTIONf_chiral_restr0.0441258
X-RAY DIFFRACTIONf_plane_restr0.0051576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.347-2.40570.357970.29623857X-RAY DIFFRACTION60
2.4057-2.47070.30831280.26495187X-RAY DIFFRACTION80
2.4707-2.54340.31941450.25185767X-RAY DIFFRACTION90
2.5434-2.62550.32121360.25716000X-RAY DIFFRACTION92
2.6255-2.71930.27221420.24545933X-RAY DIFFRACTION92
2.7193-2.82810.25091410.22445743X-RAY DIFFRACTION89
2.8281-2.95680.23811390.20825733X-RAY DIFFRACTION88
2.9568-3.11260.24021530.20986106X-RAY DIFFRACTION95
3.1126-3.30760.24941510.20226076X-RAY DIFFRACTION94
3.3076-3.56280.22021540.195959X-RAY DIFFRACTION93
3.5628-3.9210.18211390.17395758X-RAY DIFFRACTION89
3.921-4.48760.15451580.14316150X-RAY DIFFRACTION95
4.4876-5.65110.15551440.13765729X-RAY DIFFRACTION89
5.6511-38.67450.16861510.14546004X-RAY DIFFRACTION93

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