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- PDB-4b80: Mus musculus Acetylcholinesterase in complex with N-(2-Diethylami... -

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Basic information

Entry
Database: PDB / ID: 4b80
TitleMus musculus Acetylcholinesterase in complex with N-(2-Diethylamino-ethyl)-1-(4-fluoro-phenyl)-methanesulfonamide
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / INHIBITOR
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 ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A36 / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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. / 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 2.0Jul 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jul 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 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
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)123,53424
Polymers120,4682
Non-polymers3,06622
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-39.6 kcal/mol
Surface area38440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.867, 111.543, 227.589
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
#5: 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 , 7 types, 292 molecules

#2: Chemical ChemComp-A36 / N-[2-(diethylamino)ethyl]-1-(4-fluorophenyl)methanesulfonamide


Mass: 288.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H21FN2O2S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 42 % / Description: NONE
Crystal growpH: 7 / Details: 27-31 % (W/V) PEG750MME, 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: 2.5→29.01 Å / Num. obs: 70343 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 41.77 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

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

1j06


Resolution: 2.5→28.952 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML
Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED CHAIN A 259-262 AND 543-548, CHAIN B 1-3, 259-264 AND 543-548. DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING ...Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED CHAIN A 259-262 AND 543-548, CHAIN B 1-3, 259-264 AND 543-548. DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE MODELED AS ALANINES, CHAIN A 496.
RfactorNum. reflection% reflection
Rfree0.2229 1407 2 %
Rwork0.1865 --
obs0.1872 70141 99.82 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.902 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 50.02 Å2
Baniso -1Baniso -2Baniso -3
1-12.4529 Å20 Å20 Å2
2--9.1425 Å20 Å2
3----21.5955 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8356 0 198 273 8827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088835
X-RAY DIFFRACTIONf_angle_d1.08212023
X-RAY DIFFRACTIONf_dihedral_angle_d15.6633239
X-RAY DIFFRACTIONf_chiral_restr0.0781281
X-RAY DIFFRACTIONf_plane_restr0.0051566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.37421460.30386774X-RAY DIFFRACTION100
2.5893-2.69290.35441560.26566731X-RAY DIFFRACTION100
2.6929-2.81540.28981350.24656827X-RAY DIFFRACTION100
2.8154-2.96370.26451370.22666798X-RAY DIFFRACTION100
2.9637-3.14910.2431510.21596826X-RAY DIFFRACTION100
3.1491-3.39190.2771260.21256846X-RAY DIFFRACTION100
3.3919-3.73260.23551450.19426865X-RAY DIFFRACTION100
3.7326-4.27130.20581360.15066898X-RAY DIFFRACTION100
4.2713-5.37570.12731350.13126981X-RAY DIFFRACTION100
5.3757-28.95360.18371400.16977188X-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)
15.0735-1.6069-1.46871.998-0.59183.1893-0.2166-0.24110.1140.48440.1999-0.04510.09180.0073-0.0460.33940.0003-0.06040.2191-0.01910.218529.879313.007441.4702
21.6416-0.1853-0.19661.3124-0.35362.1473-0.1218-0.30630.10510.21150.0329-0.2339-0.02720.08440.0910.21610.0071-0.0360.2181-0.01620.190132.395416.377329.0978
31.3790.1256-0.9140.81540.3882.70320.0036-0.0971-0.1170.1981-0.0312-0.11820.14750.08470.04930.28180.0456-0.03850.21040.05490.273231.17018.062824.4114
41.69130.68750.53751.8956-0.34582.4723-0.11320.2759-0.2727-0.110.031-0.36410.28810.440.07910.2110.10450.01310.170.02220.21343.07228.497913.4967
53.28930.45820.75621.73450.73453.1406-0.04340.2929-0.25390.1066-0.0608-0.19040.27820.18870.13310.30280.07860.05430.25480.0590.263437.22038.0429.4446
61.68050.5124-0.25872.6912-1.61683.856-0.07240.29710.2625-0.0425-0.00020.0358-0.37770.06270.07970.20630.0048-0.00110.25420.05120.305424.13522.28071.13
75.391-3.14962.0874.3593-0.54812.6216-0.01720.76320.2592-0.3621-0.1367-0.02120.0521-0.02480.11560.2558-0.0829-0.00510.27560.04530.201822.911617.9621-8.4693
82.2236-0.0177-0.08741.96410.38913.6002-0.04590.0071-0.12490.01480.03380.22570.1638-0.64110.01120.1388-0.0424-0.02820.29210.03090.269514.381513.835816.2308
94.5213-0.48682.37818.1305-0.15375.2924-0.30640.1372-0.48120.19750.2450.85370.369-1.22630.14880.3467-0.2325-0.0110.49640.06850.43156.79841.264113.9365
101.4371-1.2155-3.0712.94962.53188.2484-0.04540.0824-0.2713-0.3701-0.19060.35720.2785-0.14080.22430.3016-0.0235-0.14470.42180.04210.294817.71086.2965-1.2817
113.3718-0.1917-1.67482.33820.32093.63560.04440.54640.1255-0.2847-0.10010.2746-0.2798-0.70270.04630.37370.0662-0.08880.459-0.14090.3008-3.71126.2791-61.8686
120.7756-0.38880.18411.10960.18291.89420.29610.2483-0.1665-0.0856-0.19110.0940.6275-0.0516-0.11540.5053-0.0287-0.06790.4563-0.1080.33335.3601-4.052-53.2024
131.82260.9065-0.58060.53460.08991.61840.06270.436-0.1048-0.3241-0.23620.27290.238-0.50210.0740.30160.0803-0.11250.48-0.13980.2894-1.21815.9556-53.9505
141.3157-0.39640.14891.70950.70492.91250.09740.1009-0.1168-0.06290.0008-0.06280.26370.3387-0.0940.24130.0105-0.04180.299-0.0440.190213.90343.1834-47.9983
155.1329-2.8505-1.94871.62391.56593.4990.11740.44080.7421-0.0692-0.0528-0.4835-0.1520.3166-0.04230.2495-0.0409-0.04090.24660.00210.308918.247214.9112-40.3318
162.02261.02990.86173.39330.47942.42880.3213-0.2192-0.36820.3945-0.0608-0.01210.79950.0866-0.28430.6442-0.0011-0.0330.2720.01020.3414.0955-6.2125-22.0888
171.39270.0450.23432.6135-0.36173.27550.1478-0.1302-0.05530.2257-0.10490.20430.1429-0.3235-0.05090.2723-0.06110.01650.3338-0.09560.25290.57755.8957-29.3366
184.0471-1.306-0.78689.0608-1.15418.79630.0688-0.19510.34080.04610.15950.6287-0.4237-0.8651-0.19380.31570.01610.06940.2608-0.04420.2442-1.643422.5898-28.9922
194.7349-0.44953.79941.2398-0.80723.3032-0.09490.3311-0.03470.1805-0.0601-0.07350.0040.31390.15580.4233-0.05990.0160.4295-0.05060.178112.692411.6875-21.7216
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 119:214)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 215:277)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 278:324)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 325:366)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 367:406)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 407:486)
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 46:86)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 87:118)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 119:298)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 299:331)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 332:382)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 383:486)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 487:513)
19X-RAY DIFFRACTION19CHAIN B AND (RESSEQ 514:542)

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