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- PDB-4b83: Mus musculus Acetylcholinesterase in complex with N-(2-Diethylami... -

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Basic information

Entry
Database: PDB / ID: 4b83
TitleMus musculus Acetylcholinesterase in complex with N-(2-Diethylamino- ethyl)-3-methoxy-benzenesulfonamide
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 / laminin binding / side of membrane / 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
Chem-B3V / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,09728
Polymers120,4682
Non-polymers3,62926
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-50.6 kcal/mol
Surface area38370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.583, 111.856, 227.783
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
Details: LIGAND N-(2-DIETHYLAMINO-ETHYL)-3-METHOXY-BENZENESULFONAMIDE
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 , 7 types, 397 molecules

#2: Chemical
ChemComp-B3V / N-[2-(diethylamino)ethyl]-3-methoxy-benzenesulfonamide


Mass: 286.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H22N2O3S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.2 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: I911-2 / 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: 2.4→29.22 Å / Num. obs: 80333 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Biso Wilson estimate: 42.29 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.3 / % 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: 2.4→29.042 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.68 / Stereochemistry target values: ML
Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED CHAIN A 259-263 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 259-263 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 AND CHAIN B 493 AND 496.
RfactorNum. reflection% reflection
Rfree0.2223 1582 2 %
Rwork0.1931 --
obs0.1937 80034 99.69 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.824 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 49.52 Å2
Baniso -1Baniso -2Baniso -3
1-10.7734 Å20 Å20 Å2
2--13.5417 Å20 Å2
3----24.315 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 228 374 8936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078845
X-RAY DIFFRACTIONf_angle_d1.07412039
X-RAY DIFFRACTIONf_dihedral_angle_d14.9263256
X-RAY DIFFRACTIONf_chiral_restr0.0761282
X-RAY DIFFRACTIONf_plane_restr0.0051565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47740.32581390.27097053X-RAY DIFFRACTION100
2.4774-2.56590.27351320.24537045X-RAY DIFFRACTION100
2.5659-2.66860.27871600.23537037X-RAY DIFFRACTION100
2.6686-2.78990.2961420.23577042X-RAY DIFFRACTION100
2.7899-2.93690.3041430.23147097X-RAY DIFFRACTION100
2.9369-3.12070.22881530.22817065X-RAY DIFFRACTION100
3.1207-3.36130.24671440.21857128X-RAY DIFFRACTION100
3.3613-3.6990.24891370.20267132X-RAY DIFFRACTION100
3.699-4.23280.20471410.16597167X-RAY DIFFRACTION100
4.2328-5.32760.13771450.14167247X-RAY DIFFRACTION100
5.3276-29.04450.20451460.1817439X-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)
10.0882-0.18910.04220.6209-0.45530.9298-0.1079-0.07220.08880.1630.0427-0.0774-0.07040.025100.35040.0137-0.02270.32040.01370.340330.51415.371332.3561
20.02120.36450.17250.5173-0.28130.9571-0.05280.0619-0.07070.02690.0048-0.06340.17910.048400.27180.04450.00560.20130.03770.276734.93925.687819.822
30.64310.18290.0285-0.0548-0.28270.8776-0.08440.1380.0085-0.00790.0119-0.02840.16910.2361-00.27740.04610.02190.23460.05870.335840.0359.217511.5148
40.3586-0.11090.51460.1749-0.16641.5274-0.06420.0997-0.0011-0.1081-0.00440.05460.0338-0.2414-00.2709-0.02-0.00130.27490.02240.339218.912617.49186.4022
50.0896-0.12570.16290.1913-0.19560.1822-0.19310.2274-0.20530.0360.22060.32570.5216-0.9062-0.00010.5266-0.18470.00310.58970.04420.54486.70791.312213.933
60.1427-0.01070.3453-0.0562-0.02250.60370.0527-0.10290.0946-0.2995-0.11370.23430.05650.0858-0.00650.3042-0.0372-0.04980.4207-0.01020.334117.62586.436-1.0784
70.14980.06540.16950.4826-0.01550.65220.05410.4536-0.0278-0.3975-0.12610.0691-0.0372-0.2271-0.00010.3910.0724-0.0790.5126-0.10160.4021-3.67886.2755-61.8803
80.1708-0.2345-0.15020.09410.27940.2390.10840.1843-0.068-0.2331-0.0933-0.03080.50730.0669-0.00010.46170.0427-0.05130.4768-0.09280.32547.15490.3329-61.5622
9-0.0280.28510.28630.16740.55731.21670.08490.224-0.0605-0.0853-0.15580.07360.2988-0.1731-0.00130.2973-0.0068-0.04030.3152-0.0760.31070.99961.6023-48.4748
100.22810.23850.05890.1385-00.15990.08130.15540.1923-0.2409-0.01-0.1086-0.13680.2165-00.38590.0256-0.01280.5112-0.01310.368414.36718.8665-55.7789
110.1203-0.2217-0.04340.24260.27230.2367-0.06520.04140.02470.0903-0.00620.017-0.1769-0.012100.30840.0216-0.0190.372-0.03820.31599.966714.1142-44.0985
120.253-0.23320.31660.3351-0.0210.2370.07630.01670.0480.14560.1572-0.06980.40890.7032-00.46290.168-0.08460.5156-0.07670.392124.4339-8.1447-46.1979
130.5166-0.2779-0.00050.3090.49310.85880.13480.03920.02970.1591-0.1044-0.04470.01240.2991-00.3667-0.0572-0.01470.3652-0.03030.391715.085210.9454-36.8177
140.45010.33680.14790.26810.29370.23780.1618-0.33650.07650.0909-0.0661-0.02170.69670.16310.00010.6577-0.0312-0.06330.37040.01950.381314.1444-5.0184-18.0758
150.0530.0406-0.06270.51820.58841.11790.09-0.03890.01570.1474-0.16030.0532-0.0214-0.2438-00.2791-0.0412-0.00640.3417-0.04990.3745-2.48258.5069-33.4091
160.0483-0.0703-0.11470.11840.12240.18530.0542-0.35980.07010.2920.06670.1847-0.325-0.35850.00010.41780.00210.02810.3452-0.03020.3862-1.133722.506-28.8858
17-0.0047-0.02780.1103-0.0665-0.1150.2546-0.1635-0.2322-0.01950.19350.10850.1046-0.02860.171500.3902-0.00920.00030.4943-0.07570.301212.574111.8498-21.5916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:142)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 143:255)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 256:331)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 332:486)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 487:513)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 514:542)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 4:45)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 46:71)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 72:158)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 159:190)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 191:237)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 238:300)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 301:341)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 342:406)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 407:486)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 487:513)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 514:542)

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