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- PDB-4b84: Mus musculus Acetylcholinesterase in complex with N-(2-Diethylami... -

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Basic information

Entry
Database: PDB / ID: 4b84
TitleMus musculus Acetylcholinesterase in complex with N-(2-Diethylamino- ethyl)-3-trifluoromethyl-benzenesulfonamide
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / 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 / presynaptic membrane / nuclear envelope / 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, catalytic domain ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15-PENTAOXAHEPTADECANE / Chem-Z5K / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsAndersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Berg, L. / Qian, W. / Ekstrom, F. / Linusson, A.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Divergent Structure-Activity Relationships of Structurally Similar Acetylcholinesterase Inhibitors.
Authors: Andersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Berg, L. / Engdahl, C. / Qian, W. / Ekstrom, F.J. / Linusson, A.
History
DepositionAug 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)123,19413
Polymers120,5242
Non-polymers2,67011
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-44.8 kcal/mol
Surface area37390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.158, 112.356, 227.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein ACETYLCHOLINESTERASE / / ACHE


Mass: 60262.039 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCDNA3.1 / Cell line (production host): HEK 293F / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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, 394 molecules

#3: Chemical
ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O5
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-Z5K / N-[2-(diethylamino)ethyl]-3-(trifluoromethyl)benzenesulfonamide


Mass: 324.362 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H19F3N2O2S
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 70.7 % / Description: NONE
Crystal growpH: 7 / Details: 27-31 % (W/V)PEG750 MME, 0.1 M HEPES PH 7.0-7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.041
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.6→29.75 Å / Num. obs: 57324 / % possible obs: 91.5 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 52.23 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1J06

1j06


Resolution: 2.6→29.082 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 1133 2 %
Rwork0.1764 --
obs0.1775 57214 90.6 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.455 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.4353 Å20 Å20 Å2
2--0.3214 Å20 Å2
3---0.1139 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8299 0 135 384 8818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098731
X-RAY DIFFRACTIONf_angle_d1.21211922
X-RAY DIFFRACTIONf_dihedral_angle_d16.2023195
X-RAY DIFFRACTIONf_chiral_restr0.0781274
X-RAY DIFFRACTIONf_plane_restr0.0051557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.71830.32331510.28277081X-RAY DIFFRACTION93
2.7183-2.86150.33911460.26057083X-RAY DIFFRACTION93
2.8615-3.04060.26981410.22747077X-RAY DIFFRACTION92
3.0406-3.27510.2731440.19817035X-RAY DIFFRACTION92
3.2751-3.60410.26941340.19257024X-RAY DIFFRACTION91
3.6041-4.12430.24481380.14766950X-RAY DIFFRACTION90
4.1243-5.19140.15131360.1266938X-RAY DIFFRACTION89
5.1914-29.08370.21511430.16666893X-RAY DIFFRACTION85
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)
13.7382-0.5745-1.77362.1587-0.60474.5265-0.1756-0.14430.17720.55740.22050.00330.0926-0.0222-0.05590.305-0.0251-0.03670.1662-0.00770.162429.996112.949441.4493
23.3114-0.11470.34561.7226-0.02611.94960.0267-0.06240.3870.1912-0.0874-0.1067-0.22730.03340.05080.27470.0445-0.02390.32050.01060.224932.610816.646429.2931
31.08180.1156-0.15270.6266-0.5742.317-0.0224-0.0496-0.25390.03710.0115-0.0960.3490.13470.00920.32720.05920.01430.14220.02530.263833.10357.72320.8056
41.43951.39230.87584.3939-2.45814.2703-0.00731.22330.6550.5179-0.5735-0.9114-0.01110.19420.35590.166-0.01160.07520.49050.11670.413652.609717.636315.2458
55.37730.05590.47731.08060.41512.1066-0.08790.3287-0.64540.1370.1986-0.27520.62160.1226-0.07560.44060.00620.08570.21630.01240.227732.15273.66589.2119
61.2943-0.06660.09280.8977-0.04923.9305-0.06990.20470.0095-0.04760.06610.14480.0561-0.2628-0.00660.1806-0.0405-0.01050.27070.03470.252319.13917.62426.3495
77.265-0.9087-1.0699.0656-2.72414.38180.1051-0.0588-1.01020.529-0.14941.12460.9417-1.74140.13880.3868-0.24260.03940.55740.01950.53317.33391.565613.5677
84.182-0.3832-3.59691.73450.70554.9543-0.4698-0.12150.1982-0.40950.37690.27030.62130.03570.110.3858-0.0446-0.1240.51220.040.269817.27716.6048-0.7575
93.94020.4573-0.28751.5835-0.16761.81590.01530.28510.5466-0.4133-0.01780.0152-0.2134-0.68960.0540.3240.1138-0.12020.7106-0.15860.2308-3.37056.3352-61.6727
101.04930.21860.40012.46960.10113.71750.12320.2669-0.1476-0.2788-0.28460.29250.596-0.16590.07180.33940.0597-0.08130.4608-0.15660.35182.6682-0.9027-53.8257
112.1876-0.61541.55892.40820.85252.42430.31680.6874-0.2269-0.2347-0.30250.17430.14840.175-0.00040.3162-0.0426-0.03020.4749-0.06740.22236.82164.4042-48.8618
121.2631-0.19520.34132.39170.45794.05510.05430.0850.047-0.15970.0016-0.1354-0.14770.2673-0.00720.2103-0.0423-00.2595-0.04040.226313.44189.6034-47.3642
130.6626-1.0494-0.51723.46762.19516.2155-0.1446-0.0674-0.50930.16260.1330.21460.97421.26050.01540.56570.2317-0.10590.4859-0.14550.272722.7587-9.2444-46.8229
143.5826-1.46890.54062.26810.97463.19230.13980.41690.4567-0.1454-0.07150.0391-0.06970.264-0.08750.2746-0.1066-0.05010.4115-0.05790.293815.56211.661-36.9279
152.33590.21410.85941.4370.494.01420.2687-0.1998-0.30260.3545-0.17510.3290.695-0.2693-0.09810.3101-0.1140.02070.18-0.12020.28044.86722.7017-26.8263
165.315-0.45062.27034.7723-3.01448.2754-0.2851-0.73581.06770.05250.19380.3031-0.0868-1.56250.02660.36070.06540.00310.5615-0.12050.366-0.355422.432-28.8043
175.2539-0.13283.72980.9255-1.00853.28060.0517-0.27980.16650.0252-0.1883-0.0648-0.05310.23380.15750.463-0.07550.02090.714-0.13780.260712.284812.0875-21.528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:45)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 46:118)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 119:255)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 256:288)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 289:331)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 332:486)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 487:513)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 514:541)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 4:45)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 46:111)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 112:170)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 171:255)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 256:300)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 301:340)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 341:486)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 487:513)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 514:542)

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