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- PDB-4b81: Mus musculus Acetylcholinesterase in complex with 1-(4-Chloro-phe... -

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Basic information

Entry
Database: PDB / ID: 4b81
TitleMus musculus Acetylcholinesterase in complex with 1-(4-Chloro-phenyl)- N-(2-diethylamino-ethyl)-methanesulfonamide
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / positive regulation of dendrite morphogenesis / acetylcholine receptor signaling pathway / choline metabolic process / osteoblast development / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / laminin binding / collagen binding / synapse assembly / response to insulin / neuromuscular junction / receptor internalization / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / synapse / 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 ...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
DI(HYDROXYETHYL)ETHER / Chem-ZN4 / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 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 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / atom_site_anisotrop / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 2.2Dec 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)123,06518
Polymers120,4682
Non-polymers2,59716
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-38.5 kcal/mol
Surface area38420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.959, 109.876, 227.926
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, 5 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 60233.984 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
#4: 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.: 3
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, 193 molecules

#2: Chemical ChemComp-ZN4 / 1-(4-chlorophenyl)-N-[2-(diethylamino)ethyl]methanesulfonamide


Mass: 304.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21ClN2O2S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


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


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.1 Å3/Da / Density % sol: 41 % / 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: I911-3 / Wavelength: 1.039
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.8→29.3 Å / Num. obs: 49067 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 52.86 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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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: 2.8→29.003 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 963 2 %
Rwork0.1965 --
obs0.1973 48890 99.71 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.069 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 63 Å2
Baniso -1Baniso -2Baniso -3
1-17.9764 Å20 Å20 Å2
2--9.7384 Å20 Å2
3----27.7148 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 165 180 8681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058745
X-RAY DIFFRACTIONf_angle_d0.9211910
X-RAY DIFFRACTIONf_dihedral_angle_d17.2413187
X-RAY DIFFRACTIONf_chiral_restr0.0661276
X-RAY DIFFRACTIONf_plane_restr0.0051551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94750.42541410.32886712X-RAY DIFFRACTION100
2.9475-3.1320.29581580.27636757X-RAY DIFFRACTION100
3.132-3.37340.30181150.23516793X-RAY DIFFRACTION100
3.3734-3.71230.24731500.20486809X-RAY DIFFRACTION100
3.7123-4.24810.22631250.17226834X-RAY DIFFRACTION100
4.2481-5.34660.18241370.15486913X-RAY DIFFRACTION100
5.3466-29.00430.20291370.17517109X-RAY DIFFRACTION99
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)
1-0.09950.0115-0.4680.2052-0.32480.8735-0.0978-0.21450.16290.25890.112-0.10840.14590.1254-0.00010.4112-0.0032-0.04950.42720.00610.332633.23212.92338.3778
20.6897-0.3060.74140.2696-0.02110.907-0.079-0.04180.07760.0516-0.0077-0.1416-0.04170.049300.3947-0.011-0.01640.3250.0020.396227.365316.15426.1251
30.16280.24930.0760.7217-0.35490.45720.1963-0.49370.15430.08810.04050.01540.6820.4420.04560.40110.1255-0.03340.28340.04620.334538.08563.255325.7345
40.12480.0444-0.01430.09630.1320.0516-0.01180.0111-0.15590.2509-0.04850.04320.3062-0.2064-0.00010.3654-0.0506-0.00610.26560.05360.340925.72370.62921.6739
50.1542-0.22920.07350.1282-0.23550.61560.11520.5208-0.3887-0.0601-0.0933-0.00570.2950.17340.00010.49470.10730.04180.35980.00680.370142.133510.50197.4723
60.21970.15040.00260.3102-0.46491.4783-0.01650.30330.01760.0704-0.0042-0.07750.24920.273100.35360.02210.02690.3560.02920.410439.2588.673811.6868
70.29590.0743-0.44160.3115-0.1460.4102-0.01560.29860.2406-0.37320.0318-0.0661-0.29380.0117-0.00010.44590.01090.00190.50830.07440.497326.037721.4594-3.9128
80.854-0.00240.4250.48750.05421.0139-0.08430.0576-0.0679-0.10210.02820.14610.0125-0.3155-00.3193-0.037-0.01150.3830.0240.370314.994815.029210.8805
90.0873-0.0290.15230.1171-0.0670.1056-0.25030.4204-0.4885-0.01670.08650.45090.1399-0.08620.00040.583-0.1834-0.05040.49380.02820.55776.09370.921113.9493
100.1973-0.60180.10050.6111-0.54080.52660.2806-0.41910.2948-0.5544-0.06970.02410.39790.01790.06670.3021-0.0691-0.14650.7316-0.04620.420217.33355.999-1.228
110.2556-0.05080.33770.18670.42310.7611-0.13830.4436-0.1002-0.1818-0.0667-0.0378-0.0404-0.15340.00020.47340.0393-0.06890.6004-0.04750.4989-3.62386.2001-62.0388
12-0.13290.11890.28711.05790.67441.48180.15590.3308-0.0746-0.1535-0.20170.01030.30930.0644-0.00110.3391-0.0053-0.03670.3753-0.04580.31842.48531.1728-51.7948
130.2388-0.5546-0.02870.5533-0.07531.37840.05160.0756-0.0552-0.08340.01370.04380.05910.279300.36820.0412-0.05430.4489-0.05070.408917.90935.0111-46.9468
14-0.19720.19250.07340.16230.07590.18360.0231-0.5281-0.07990.26140.0649-0.06130.5913-0.12670.00510.7887-0.0622-0.03650.39950.0170.53096.3549-4.2751-27.2483
150.14160.23620.07970.6691-0.03361.75680.1996-0.07220.07270.1523-0.2018-0.02390.2806-0.054600.4174-0.0219-0.00690.3689-0.06460.37734.42083.7837-27.5554
160.36330.3407-0.15010.2060.09930.8020.1023-0.23720.067-0.0608-0.02590.0998-0.02560.030900.6508-0.0295-0.0240.4764-0.04850.42626.561816.1061-24.8741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:71)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 72:158)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 159:190)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 191:228)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 229:255)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 256:331)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 332:382)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 383:486)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 487:513)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 514:542)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 4:45)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 46:158)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 159:324)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 325:355)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 356:486)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 487:543)

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