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- PDB-4b82: Mus musculus Acetylcholinesterase in complex with N-(2-Diethylami... -

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Basic information

Entry
Database: PDB / ID: 4b82
TitleMus musculus Acetylcholinesterase in complex with N-(2-Diethylamino- ethyl)-2-fluoranyl-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 / 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, 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
Chem-B3Z / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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 / Structure summary
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / atom_site_anisotrop / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.1Sep 4, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Dec 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)122,93419
Polymers120,4682
Non-polymers2,46617
Water16,826934
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-44.2 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.460, 111.858, 226.930
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 , 4 types, 948 molecules

#2: Chemical ChemComp-B3Z / N-[2-(diethylamino)ethyl]-2-fluoranyl-benzenesulfonamide


Mass: 274.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19FN2O2S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 934 / 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: 2.2 Å3/Da / Density % sol: 43 % / 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: I911-3 / Wavelength: 1.039
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 30, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.1→29.19 Å / Num. obs: 120032 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 36.29 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.7 / % possible all: 98

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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: 2.1→28.81 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 2414 2 %
Rwork0.1909 --
obs0.1914 119900 99.86 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.867 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 40.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.7809 Å20 Å20 Å2
2--2.8417 Å20 Å2
3----2.0608 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 158 934 9428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048799
X-RAY DIFFRACTIONf_angle_d0.911985
X-RAY DIFFRACTIONf_dihedral_angle_d18.5063202
X-RAY DIFFRACTIONf_chiral_restr0.0641281
X-RAY DIFFRACTIONf_plane_restr0.0041564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14290.27211510.2576807X-RAY DIFFRACTION99
2.1429-2.18940.24751420.24256827X-RAY DIFFRACTION100
2.1894-2.24030.27321570.23486799X-RAY DIFFRACTION100
2.2403-2.29640.24311430.22076838X-RAY DIFFRACTION100
2.2964-2.35840.22961460.21616822X-RAY DIFFRACTION100
2.3584-2.42780.27671390.22326854X-RAY DIFFRACTION100
2.4278-2.50610.23161190.21536911X-RAY DIFFRACTION100
2.5061-2.59560.22151470.2076855X-RAY DIFFRACTION100
2.5956-2.69950.24211540.20076860X-RAY DIFFRACTION100
2.6995-2.82220.24551340.19666878X-RAY DIFFRACTION100
2.8222-2.97090.21351460.196906X-RAY DIFFRACTION100
2.9709-3.15680.20621440.1936909X-RAY DIFFRACTION100
3.1568-3.40020.22781310.19466936X-RAY DIFFRACTION100
3.4002-3.74170.20131440.18336954X-RAY DIFFRACTION100
3.7417-4.28160.19511390.15767004X-RAY DIFFRACTION100
4.2816-5.38860.18411370.14987060X-RAY DIFFRACTION100
5.3886-28.81310.20021410.21027266X-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)
10.9587-0.54010.04251.3296-0.63322.6287-0.0809-0.11530.05780.2510.0042-0.036-0.18970.11690.08810.1706-0.0238-0.03640.12010.01050.164633.023916.573534.5979
22.60330.2183-1.04860.78080.07242.4457-0.0238-0.14540.01040.19430.01510.0001-0.0107-0.09580.02310.24490.0254-0.01230.20970.02760.223926.326114.54529.895
31.27730.8799-1.27941.0332-0.73512.9817-0.1582-0.1507-0.280.1134-0.0296-0.14860.3350.27650.1560.27040.0472-0.00990.21950.03680.275837.4226.829925.4021
41.48650.11520.13620.7737-0.28451.8639-0.06360.0807-0.0995-0.063-0.0055-0.12980.31950.17030.0820.23250.04910.01570.15060.0120.234436.95277.670913.6884
50.7081-0.0260.20180.8884-0.4712.4178-0.04730.01790.0136-0.02480.01310.0903-0.034-0.27540.02970.1585-0.0136-0.02020.217-0.00190.226318.581417.34216.8237
63.0498-0.04181.27266.1053-1.72931.00760.0973-0.3371-0.26260.51-0.01690.86610.3006-1.11190.00670.3046-0.28090.03690.54460.06110.37157.2450.871214.8236
73.537-0.8959-2.04872.07441.20894.9886-0.02320.2064-0.2282-0.1704-0.1090.26150.3039-0.45250.14210.2368-0.0718-0.06940.26070.01370.227217.60486.2716-0.5407
84.61170.0332-2.16062.1451-0.60864.673-0.10840.4344-0.0571-0.3393-0.23830.5121-0.1484-0.89140.05410.31210.0744-0.12620.5037-0.14990.414-10.02937.7693-61.3319
90.9344-0.0523-0.15451.24340.00463.01150.07670.147-0.1681-0.1119-0.10350.10730.4527-0.02620.02590.26320.0037-0.05310.2258-0.10680.23886.292-3.362-54.3494
101.26870.0247-0.30671.16780.74252.40070.14570.197-0.168-0.1967-0.18780.35080.1103-0.39030.01020.2025-0.0298-0.05060.2467-0.07420.22970.46274.0705-50.1009
118.1493-4.86692.7125.1383-1.41993.07610.1850.3470.1864-0.3746-0.1394-0.1644-0.13640.2474-0.06850.2821-0.0132-0.00590.3241-0.05720.236413.74718.5215-55.2235
121.095-0.27660.31181.36430.37092.11780.11470.2073-0.05720.072-0.0668-0.1260.23260.3311-0.04740.18760.008-0.03960.2369-0.04270.20617.07623.9179-42.2679
131.1994-0.08020.60140.87680.19792.0280.1567-0.1003-0.16060.1858-0.10480.16240.4015-0.263-0.07030.2765-0.08880.00960.205-0.04580.2344.57122.3653-26.38
141.17860.5531-2.52146.05670.46847.5570.04270.0820.2993-0.06890.02120.6176-0.4419-0.6335-0.01190.19940.03350.0150.1974-0.0630.3056-1.737722.1095-28.2205
154.1930.13611.59172.10840.67963.92520.085-0.3050.12330.2291-0.0239-0.14930.17430.3318-0.02320.2492-0.04720.02530.1867-0.00830.125512.96711.2427-21.2484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:86)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 87:142)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 143:190)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 191:331)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 332:486)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 487:513)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 514:542)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 4:32)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 33:86)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 87:158)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 159:191)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 192:341)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 342:486)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 487:513)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 514:543)

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