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- PDB-9omt: X-ray structure of paraoxon (POX)-inhibited human acetylcholinest... -

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Basic information

Entry
Database: PDB / ID: 9omt
TitleX-ray structure of paraoxon (POX)-inhibited human acetylcholinesterase (hAChE) in complex with bis-oxime reactivator LG-1922
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / homodimer / reactivator complex / organophosphate-inhibited acetylcholinesterase
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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / DIETHYL PHOSPHONATE / NITRATE ION / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsKovalevsky, A. / Radic, Z. / Gerlits, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS120839 United States
CitationJournal: Chem.Biol.Interact. / Year: 2025
Title: Kinetic and structural evidence for specific DMSO interference with reversible binding of uncharged bis-oximes to hAChE and their reactivation kinetics of OP-hAChE.
Authors: Kolic, D. / Gerlits, O. / Kucharski, M. / Gorecki, L. / Joiner, N. / Kovalevsky, A. / Radic, Z.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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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)121,90911
Polymers120,5762
Non-polymers1,3339
Water1,964109
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,90911
Polymers120,5762
Non-polymers1,3339
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z+1/31
Buried area5240 Å2
ΔGint5 kcal/mol
Surface area38810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.367, 124.367, 128.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 60287.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase

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Non-polymers , 6 types, 118 molecules

#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-A1CDA / (2E)-2-(hydroxyimino)-N-{3-[(3R)-3-(2-{[(2E)-2-(hydroxyimino)acetyl]amino}ethyl)piperidin-1-yl]propyl}acetamide


Mass: 327.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N5O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
Nonpolymer detailsThe bis-oxime reactivator LG-1922 was prepared as a racemic mixture. The chirality of the bound ...The bis-oxime reactivator LG-1922 was prepared as a racemic mixture. The chirality of the bound compound cannot be unequivocally established given the resolution of the data, thus the ligand was refined with the chirality that best fits the electron density (A1CDA).

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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: 4.75 Å3/Da / Density % sol: 74.13 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 100 mM potassium nitrate, 100 mM HEPES pH 7.5, 11 % PEG 3350

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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 X 6M / Detector: PIXEL / Date: Apr 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 56220 / % possible obs: 92.7 % / Redundancy: 3.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.038 / Rrim(I) all: 0.08 / Net I/σ(I): 15.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 5754 / CC1/2: 0.443 / Rpim(I) all: 0.664 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
PHASERphasing
HKL-3000data scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.704→49.661 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 2542 4.91 %random
Rwork0.1957 ---
obs0.1976 51792 85.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.704→49.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 86 109 8571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048790
X-RAY DIFFRACTIONf_angle_d0.65112011
X-RAY DIFFRACTIONf_dihedral_angle_d14.9795148
X-RAY DIFFRACTIONf_chiral_restr0.0451264
X-RAY DIFFRACTIONf_plane_restr0.0051594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7042-2.75620.365440.3316961X-RAY DIFFRACTION30
2.7562-2.81250.4011960.31711640X-RAY DIFFRACTION52
2.8125-2.87360.34541530.28862441X-RAY DIFFRACTION77
2.8736-2.94040.38341820.27182954X-RAY DIFFRACTION92
2.9404-3.0140.32781570.25312967X-RAY DIFFRACTION94
3.014-3.09540.31251480.24863031X-RAY DIFFRACTION94
3.0954-3.18650.30181650.24793000X-RAY DIFFRACTION93
3.1865-3.28940.25511540.2333003X-RAY DIFFRACTION93
3.2894-3.40690.21851540.21712938X-RAY DIFFRACTION93
3.4069-3.54330.25621480.2023001X-RAY DIFFRACTION92
3.5433-3.70450.2131260.20082975X-RAY DIFFRACTION92
3.7045-3.89970.22181890.18622929X-RAY DIFFRACTION92
3.8997-4.14390.23081170.16933028X-RAY DIFFRACTION93
4.1439-4.46370.171840.15622875X-RAY DIFFRACTION91
4.4637-4.91250.19641290.14492957X-RAY DIFFRACTION92
4.9125-5.62250.21251350.16662911X-RAY DIFFRACTION91
5.6225-7.08050.21391150.18342877X-RAY DIFFRACTION89
7.0805-49.660.16731460.16822762X-RAY DIFFRACTION86

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