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- PDB-7r3c: VX-inhibited acetylcholinesterase in complex with 2-((hydroxyimin... -

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Basic information

Entry
Database: PDB / ID: 7r3c
TitleVX-inhibited acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / ternary complex / reactivator
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 / side of membrane / synaptic cleft / laminin binding / 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-I1X / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.40000421983 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 7, 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)122,55617
Polymers119,7412
Non-polymers2,81515
Water5,314295
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)79.154, 112.094, 226.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59870.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VX phosphonylation product covalently attached to Ser203
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Plasmid: PCDNA3.1 / Cell line (production host): HEK293F / 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: 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, 308 molecules

#2: 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.: 7 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O4
#6: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 27-30 % (w/v) PEG750MME 0.1 M HEPES pH 7.0-7.1

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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: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→29.1 Å / Num. obs: 78034 / % possible obs: 98.1 % / Redundancy: 6 % / Biso Wilson estimate: 39.8566132128 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 11420 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.40000421983→29.0277342368 Å / SU ML: 0.213495052205 / Cross valid method: FREE R-VALUE / σ(F): 1.33593122603 / Phase error: 22.2497383232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.196769530573 1547 1.98715478484 %
Rwork0.16891694679 76303 -
obs0.169471079 77850 97.6971826567 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.6114750798 Å2
Refinement stepCycle: LAST / Resolution: 2.40000421983→29.0277342368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 191 295 8812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006680657961478817
X-RAY DIFFRACTIONf_angle_d0.91704119118212017
X-RAY DIFFRACTIONf_chiral_restr0.05528102524751279
X-RAY DIFFRACTIONf_plane_restr0.00624168776521568
X-RAY DIFFRACTIONf_dihedral_angle_d10.28777849857074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.40000421983-2.47740.28149536191280.2237897226276937X-RAY DIFFRACTION98.783557047
2.4774-2.56590.251354444141360.2024093007446891X-RAY DIFFRACTION98.7631763879
2.5659-2.66860.2218964784261570.1940926344196928X-RAY DIFFRACTION98.6631388386
2.6686-2.790.2191310194861420.1920164908856929X-RAY DIFFRACTION98.6467633929
2.79-2.93690.2688117985351400.1935262061126910X-RAY DIFFRACTION97.9030690182
2.9369-3.12070.2199821016441540.1988973441876930X-RAY DIFFRACTION98.4299013478
3.1207-3.36130.2307028246551360.1985516873376896X-RAY DIFFRACTION97.8297161937
3.3613-3.6990.207352169771380.1723550798586929X-RAY DIFFRACTION97.6644555003
3.699-4.23280.1766876466331350.1469300867266938X-RAY DIFFRACTION97.076585232
4.2328-5.32750.1412701719451370.1317321188526957X-RAY DIFFRACTION96.4645091107
5.3275-29.02773423680.1684346137471440.1576892888277058X-RAY DIFFRACTION94.6884038917
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)
11.932976896060.0356273721688-0.393247297671.30896099814-0.5436133220273.41536960101-0.120715114901-0.2053535538230.1269450845420.2810264992870.0356930835626-0.034523010427-0.1148138904340.02032195485640.06376487131120.3156779055050.00846315278489-0.02358217341680.2686274987220.009735697487450.23968908988431.025936311915.25631098831.3828353365
22.093232230490.749936044676-1.028707753391.7519935167-1.132764320725.10188591484-0.172247530575-0.23499224234-0.2677777534380.0743449260327-0.0533505384989-0.3472791341660.6425383339350.3670301349380.2375663250060.4129379065270.115095070021-0.0259819397210.2802845182130.06521113198390.35823443516939.0531084673.9820567976325.5722095251
33.061552625810.713189770203-0.2217875570761.4541744358-0.734695360312.96629188531-0.1038268995920.163855265974-0.0646700146205-0.136711612048-0.0179772233722-0.1909526196610.2172087322750.2436420336390.1595790668980.3262646052930.08071651330780.004618880390930.2658705712980.02927817733890.25149016623939.096357225110.380793569314.1209296437
45.09633305603-0.2610880075230.0926881828742.815798073940.8536255348162.84606541779-0.1958490227830.218636624933-1.024938556020.03871086518840.101438815544-0.02070291837020.8361190085650.1259944799560.0604444860690.5840518528860.01417507220360.07395955268230.3830915331190.01936180957660.37616079586430.7774954004-1.1469120072911.41008469
52.70832156123-0.4386175268260.8796388587035.38974697574-1.826095553633.34022849874-0.01571220367760.2661867705790.152203529401-0.109160062246-0.0280211526681-0.0197081669802-0.173037478052-0.00855911588250.0464254427580.225120697896-0.0316831699298-0.02283804971890.3683338322620.08204124666750.2461038060326.652568294821.7758806146-3.90432738491
61.33444994549-0.4794954245430.1581660255891.17075298807-0.4775569318594.12925847872-0.05892039605520.0690192099308-0.0129162107655-0.07761096173130.03395988736130.2118745078740.101062381776-0.4976956422060.05728554655760.251237484708-0.0612886560938-0.02267711040080.3604347704150.01046014560460.29984460773715.727860496215.620343156210.7959355279
76.7249798128-0.5293109204880.2938448652112.40600837257-2.920194671015.22297194511-0.159909968044-0.0201968191817-0.6459835101650.3035674636220.1430229314030.7103691195590.914437210744-1.488490801220.06036837114210.548107468235-0.2444728732870.03528931272380.5922177476740.05815371077010.4493758888917.307316784641.4143000259413.6552558769
82.88284954931-0.839265744718-3.682196461493.039649555822.535220185928.806977824740.0930947114788-0.0270621336915-0.166791011394-0.37345549094-0.1118887667410.08526449503210.3266201737940.1587240152170.04946800211280.4880557742360.00143474033798-0.1184796470580.533111956180.005201020149390.3125306243217.92792898886.32717046663-1.13152128351
95.63915474051-1.17180435607-1.540952243532.338504741180.3494073722054.692704913610.01384862157960.6116152918280.10853125827-0.270183090806-0.2029806728140.330322065306-0.255109354902-0.8045364058370.1676522028370.4468453060730.0496836011581-0.09947030334090.499441357885-0.1556888145170.356225273528-3.706920788026.02312249269-61.3326272388
100.494792256613-0.526198762010.2128170912721.71806691835-0.5136789527466.698290969140.1460817932440.115490162617-0.16829872532-0.109499116319-0.09634043022380.2023464879670.771924592655-0.216801348581-0.04784347204550.449438185376-0.0334030855242-0.06847484823860.447669377916-0.118183867210.3405346318745.36278517148-4.28449163895-52.8326141148
111.9189138374-0.4863593557550.1041831863751.987434066670.8122529820363.083848211220.1032169320530.146831360916-0.110894681021-0.0276313969228-0.06751911263670.008511716436490.2054581683640.165466836566-0.03086055768360.3578800465980.00973460345547-0.02536614229120.375798397523-0.07519457339340.23203440862711.24293199323.47973527093-48.6220120146
123.57898752199-1.59633664297-1.196457890231.602277186741.68335020284.631484130640.2653208932940.3228466417210.551816553904-0.0453403901317-0.0372077358235-0.370272708566-0.3045191577480.624694398253-0.2560168549430.395112757287-0.0722224724368-0.01734959245450.459715882283-0.02581033661610.39200395496518.484411269814.1259450501-40.0685058208
133.880480898150.6825386469690.752178351642.341692403290.09252148613844.748838623170.300089988905-0.0961125071144-0.5112937917510.5449766774220.01670602568920.009869554761580.96249595740.0569030344554-0.2140002510190.8073822641070.0128821296731-0.07321712924090.344513944894-0.03230412675340.36257405618514.3542247502-6.08496066273-21.909506874
142.04662164871-0.1844268797150.1813901362631.76541678811-0.3789008739383.501529381230.184413217712-0.263539332356-0.08847373021640.512251068853-0.1777745364720.04935132466680.3539903659920.1153157641730.01058253255460.458546352886-0.07920576844430.003079584445570.3751523439-0.09185893406690.2356264970547.956957294714.91817025277-23.6439764258
151.453254896810.08104882354280.1142034964223.76469647419-0.6092964560844.2997714075-0.0208784437909-0.105825961222-0.0520363774060.147177518899-0.09478704957290.5123931610850.260357120663-0.963252645820.02456343338450.329319579168-0.04899428857250.04236428188720.58752919061-0.1538227543860.395877995134-7.517446612626.8773485596-35.140798581
166.32381900604-0.0680631225220.7439273552734.51388521128-2.828752369615.34566964334-0.0455814522309-0.4369102168560.6739955238090.1284105743830.1043318222210.493960481918-0.634875126965-0.3219646369090.04562417137240.4884296316550.0322606967168-0.01327963920850.427961081276-0.145339364790.400461748221-0.8469769886122.4693437248-28.6451967136
176.508282373020.1505439060215.987686407081.54247066256-0.3125283140335.92246914241-0.03705453976460.355791619036-0.0225604019610.0777065541737-0.126348195395-0.043262289950.002118766513380.577592755170.1270195593310.549940651901-0.09213074703220.05710044104220.444181540588-0.04777428624960.21314771984512.83882458511.7232403468-21.5370650108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 298 )
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 331 )
5X-RAY DIFFRACTION5chain 'A' and (resid 332 through 382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 486 )
7X-RAY DIFFRACTION7chain 'A' and (resid 487 through 513 )
8X-RAY DIFFRACTION8chain 'A' and (resid 514 through 542 )
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 297 )
12X-RAY DIFFRACTION12chain 'B' and (resid 298 through 331 )
13X-RAY DIFFRACTION13chain 'B' and (resid 332 through 382 )
14X-RAY DIFFRACTION14chain 'B' and (resid 383 through 440 )
15X-RAY DIFFRACTION15chain 'B' and (resid 441 through 486 )
16X-RAY DIFFRACTION16chain 'B' and (resid 487 through 513 )
17X-RAY DIFFRACTION17chain 'B' and (resid 514 through 542 )

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