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- PDB-7r2f: Structure of tabun inhibited acetylcholinesterase in complex with... -

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Basic information

Entry
Database: PDB / ID: 7r2f
TitleStructure of tabun inhibited acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Complex / tabun phosphylated / Reactivator
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / collagen binding / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / 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
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / Chem-I1X / 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
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 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 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)123,05121
Polymers119,7992
Non-polymers3,25219
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint63 kcal/mol
Surface area38420 Å2
Unit cell
Length a, b, c (Å)78.826, 110.755, 227.569
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, 4 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59899.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Tabun phosphylation product covalently attached to Ser203
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Plasmid: PCDNA3.1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P21836, 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.: 2 / 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 , 4 types, 269 molecules

#3: Chemical ChemComp-I1X / 4-methyl-3-nitro-~{N}-[(2~{E},4~{E})-5-[2-[(oxidanylamino)methyl]pyridin-1-yl]penta-2,4-dienyl]benzamide


Mass: 371.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#5: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 4.19 Å3/Da / Density % sol: 70.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 28-30 % /w7v) 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: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 85474 / % possible obs: 96.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 42.52 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 12569 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.3→46.1411 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1688 1.98 %
Rwork0.1722 83505 -
obs0.1728 85193 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.78 Å2 / Biso mean: 57.57 Å2 / Biso min: 27.85 Å2
Refinement stepCycle: final / Resolution: 2.3→46.1411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 194 252 8784
Biso mean--89.97 52.88 -
Num. residues----1068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079543
X-RAY DIFFRACTIONf_angle_d1.08313106
X-RAY DIFFRACTIONf_chiral_restr0.0421429
X-RAY DIFFRACTIONf_plane_restr0.0061729
X-RAY DIFFRACTIONf_dihedral_angle_d16.093546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36770.31661340.27157002713697
2.3677-2.44410.34371350.24367011714697
2.4441-2.53140.27451370.22356973711097
2.5314-2.63280.23291510.21386969712097
2.6328-2.75260.26131450.20946980712597
2.7526-2.89770.25241470.20646966711396
2.8977-3.07920.24791510.20536955710696
3.0792-3.31690.22251400.19646943708395
3.3169-3.65060.19151330.16856926705995
3.6506-4.17850.16861340.14656915704994
4.1785-5.26330.13841410.1286915705693
5.2633-46.14110.19851400.15366950709091
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)
11.87350.1759-0.35491.3152-0.33243.4595-0.0962-0.22430.14150.22080.06420.047-0.1046-0.0540.02960.40080.0204-0.02430.31460.02880.259230.464915.16131.5171
22.52150.8687-0.44611.2765-0.80133.0575-0.09790.1042-0.1377-0.09890.0084-0.14730.36590.2160.11240.40770.08810.00120.26020.02260.265239.138.773216.9109
35.7543-0.24460.29981.4279-1.97884.3644-0.1291-0.01-0.7268-0.20450.22190.13570.5997-0.1709-0.07820.5467-0.03860.02070.389-0.06010.268927.73163.99210.4732
41.2246-0.2348-0.43841.2343-0.44145.1434-0.01810.14350.0584-0.15220.04930.15090.0116-0.4962-0.03540.3047-0.0432-0.06970.41830.01520.325218.494617.16676.3195
58.3204-2.360.58025.1542-1.648.0356-0.31060.0484-0.81230.19610.08410.85640.96-1.64150.29990.588-0.27940.01330.67110.04080.48727.19281.208213.5952
64.3875-1.7549-3.49913.0432.2933.5827-0.17190.3988-0.2773-0.30220.00380.20450.3919-0.3590.14550.5776-0.0314-0.14960.74650.02870.371817.53436.3853-0.5849
71.4526-0.3956-0.13891.5890.54064.10160.13720.2901-0.1524-0.1377-0.23420.2920.2789-0.48630.09640.4843-0.0189-0.07690.549-0.13650.35490.48381.3783-56.9918
81.9389-0.6777-0.06092.39610.93923.60260.11490.0771-0.06990.0663-0.0331-0.13160.18240.3282-0.09420.44670.0118-0.04450.446-0.0640.278913.69443.1533-47.9666
93.8625-1.5424-1.27371.3652-0.83056.20970.11610.22020.19540.1947-0.0053-0.24770.03870.3168-0.09210.4519-0.0688-0.09180.4117-0.10980.306914.814910.6707-36.8494
102.0177-0.24290.58271.9221-0.28292.8680.2435-0.3286-0.36250.5562-0.1027-0.01280.65670.0181-0.15570.7369-0.0621-0.05030.4396-0.04220.353911.4061-0.0931-22.2128
112.93351.29160.65875.29720.12895.2839-0.0067-0.02570.1023-0.0292-0.1590.67710.0381-0.86680.16340.38790.00990.04350.5446-0.11440.3538-5.247311.3241-33.4828
128.9113-0.65187.2321.8698-0.69266.19670.07480.2425-0.32690.324-0.0724-0.02630.14330.39610.00450.6313-0.07540.02170.4425-0.01570.232712.214211.3273-21.9909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 158 )A1 - 158
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 300 )A159 - 300
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 341 )A301 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 486 )A342 - 486
5X-RAY DIFFRACTION5chain 'A' and (resid 487 through 513 )A487 - 513
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 542 )A514 - 542
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 111 )B4 - 111
8X-RAY DIFFRACTION8chain 'B' and (resid 112 through 300 )B112 - 300
9X-RAY DIFFRACTION9chain 'B' and (resid 301 through 341 )B301 - 341
10X-RAY DIFFRACTION10chain 'B' and (resid 342 through 440 )B342 - 440
11X-RAY DIFFRACTION11chain 'B' and (resid 441 through 513 )B441 - 513
12X-RAY DIFFRACTION12chain 'B' and (resid 514 through 543 )B514 - 543

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