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- PDB-7r02: Mus musculus acetylcholinesterase in complex with N-(3-(diethylam... -

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Basic information

Entry
Database: PDB / ID: 7r02
TitleMus musculus acetylcholinesterase in complex with N-(3-(diethylamino)propyl)-4-methyl-3-nitrobenzamide
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Complex / inhibitor
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-9YU / Chem-I62 / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsForsgren, N. / Lindgren, C. / Edvinsson, L. / Linusson, A. / Ekstrom, F.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Other government Sweden
Swedish Research Council Sweden
CitationJournal: Chemistry / Year: 2022
Title: Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase.
Authors: Lindgren, C. / Forsgren, N. / Hoster, N. / Akfur, C. / Artursson, E. / Edvinsson, L. / Svensson, R. / Worek, F. / Ekstrom, F. / Linusson, A.
History
DepositionFeb 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 2.0Jun 15, 2022Group: Database references / Non-polymer description / Category: chem_comp / citation / citation_author
Item: _chem_comp.formula / _citation.page_first ..._chem_comp.formula / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.1Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)122,72321
Polymers119,5292
Non-polymers3,19419
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.852, 111.105, 227.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Acetylcholinesterase / / AChE


Mass: 59764.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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

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Non-polymers , 5 types, 361 molecules

#2: Chemical ChemComp-I62 / ~{N}-[(~{E})-3-(diethylamino)prop-2-enyl]-4-methyl-3-nitro-benzamide


Mass: 292.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-9YU / 2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol


Mass: 340.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32O8
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.16 Å3/Da / Density % sol: 70.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 28-30% (w/v) PEG750MME 0.1 M HEPES pH 6.9-7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.03763 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03763 Å / Relative weight: 1
ReflectionResolution: 2.3→29.6 Å / Num. obs: 89430 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 40.98 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.416 / Num. unique obs: 12913 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.3→28.71 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 1760 1.97 %
Rwork0.1692 87380 -
obs0.1695 89140 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.91 Å2 / Biso mean: 53.5864 Å2 / Biso min: 26.15 Å2
Refinement stepCycle: final / Resolution: 2.3→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8339 0 211 346 8896
Biso mean--84.31 51.96 -
Num. residues----1072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.23791320.220666436775100
2.36-2.430.24611330.205666526785100
2.43-2.510.23731180.193166426760100
2.51-2.60.2041380.181666506788100
2.6-2.70.18131490.180566546803100
2.7-2.830.23021350.188966836818100
2.83-2.980.2181380.192166866824100
2.98-3.160.20591540.194167096863100
3.16-3.410.19811130.187767216834100
3.41-3.750.19891490.166167326881100
3.75-4.290.1731300.146168056935100
4.29-5.40.12721340.13668426976100
5.4-28.710.17191370.16796961709898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.068-0.649-0.77481.8657-0.88474.2354-0.1283-0.4-0.04110.39560.06260.04820.0050.05240.06330.4513-0.0199-0.03630.36090.00140.313530.468112.679640.8482
21.54060.0314-0.46561.066-0.16352.8973-0.0576-0.1196-0.04360.07120.0012-0.05910.17120.06570.06280.32770.011-0.01740.29990.04960.321232.583310.792224.013
33.86452.09921.99892.86511.06474.3727-0.09510.23550.1846-0.1752-0.0689-0.3164-0.24910.64410.1910.2770.01730.05110.42270.07510.371748.146317.701811.9349
44.76560.20760.70232.28090.95052.194-0.11070.0229-0.75720.05740.0745-0.12740.76290.0795-0.00760.57580.01880.05840.31540.03950.349230.6078-1.296711.3739
51.8747-0.2033-0.1742.7165-0.27265.2371-0.06150.29080.1599-0.19630.04480.0557-0.250.11410.03570.2966-0.0443-0.03350.3910.06910.352326.225921.7301-3.8994
61.1716-0.0768-0.14481.2248-0.51874.4496-0.03910.0615-0.0315-0.04530.04830.22870.0571-0.6153-0.02470.2198-0.0453-0.0310.37230.00760.333215.499315.0610.987
76.6154-1.68190.93719.0675-1.90385.3179-0.1729-0.0563-0.70430.4451-0.02971.0750.7856-1.60840.2760.4956-0.29640.00810.63840.02770.52657.05441.14113.5715
89.1061-3.6254-5.72483.77623.3484.97570.08050.0401-0.3287-0.3338-0.14290.18810.044-0.12750.05280.4676-0.0244-0.12560.5650.00940.334518.24316.2604-1.5392
95.4635-1.2352-2.97211.9660.76735.00450.05240.37140.1194-0.346-0.14310.3431-0.1699-0.81550.01820.49320.0337-0.12330.5839-0.13720.4306-3.0146.0047-61.8142
101.2279-0.29430.11331.78220.41673.6910.10740.169-0.1856-0.0921-0.15630.29940.3461-0.38680.03510.3527-0.039-0.06330.4269-0.10590.34971.46281.0096-51.666
115.0488-3.15861.59524.2914-0.41073.10960.12610.53690.0391-0.1041-0.153-0.0623-0.06860.37250.02210.38450.0033-0.02550.4483-0.06920.261112.32886.8437-54.1065
122.2646-1.07830.19752.48120.44723.38910.08060.1060.07440.0772-0.007-0.1915-0.14260.3472-0.05490.3118-0.0342-0.01850.3697-0.04450.261814.99278.6608-44.1062
131.7085-1.3191-0.13434.02861.49325.36610.13620.0905-0.28980.1611-0.0034-0.15450.80060.7894-0.14160.57550.1644-0.13870.5406-0.09870.464523.056-9.8181-47.7004
144.5813-2.237-1.47111.24270.72164.3620.17460.33980.66560.0788-0.0884-0.4213-0.43620.4349-0.07380.3961-0.0786-0.05940.4297-0.04040.425818.273514.3867-40.2684
151.7132-0.3810.98311.7028-0.14343.21350.1926-0.181-0.24040.2435-0.10450.19230.4977-0.2954-0.09220.4642-0.08790.02040.3671-0.06940.33855.16211.9477-26.6855
167.6967-1.23630.51514.5025-3.19775.51620.0522-0.4090.809-0.00860.01590.4135-0.4673-0.4849-0.03390.4940.01920.01040.3415-0.10410.4212-0.949222.4832-28.7797
179.2903-1.11454.71541.8443-0.06954.16470.02970.3432-0.44680.0970.0301-0.04310.08730.3307-0.10420.4807-0.06570.02250.3593-0.00880.250313.203311.1954-21.6106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )A1 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 254 )A46 - 254
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 298 )A255 - 298
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 331 )A299 - 331
5X-RAY DIFFRACTION5chain 'A' and (resid 332 through 382 )A332 - 382
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 486 )A383 - 486
7X-RAY DIFFRACTION7chain 'A' and (resid 487 through 513 )A487 - 513
8X-RAY DIFFRACTION8chain 'A' and (resid 514 through 543 )A514 - 543
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 45 )B4 - 45
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 142 )B46 - 142
11X-RAY DIFFRACTION11chain 'B' and (resid 143 through 190 )B143 - 190
12X-RAY DIFFRACTION12chain 'B' and (resid 191 through 254 )B191 - 254
13X-RAY DIFFRACTION13chain 'B' and (resid 255 through 297 )B255 - 297
14X-RAY DIFFRACTION14chain 'B' and (resid 298 through 331 )B298 - 331
15X-RAY DIFFRACTION15chain 'B' and (resid 332 through 486 )B332 - 486
16X-RAY DIFFRACTION16chain 'B' and (resid 487 through 513 )B487 - 513
17X-RAY DIFFRACTION17chain 'B' and (resid 514 through 543 )B514 - 543

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