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- PDB-4btl: Aromatic interactions in acetylcholinesterase-inhibitor complexes -

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Basic information

Entry
Database: PDB / ID: 4btl
TitleAromatic interactions in acetylcholinesterase-inhibitor complexes
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / 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-5GZ / Chem-PE3 / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAndersson, C.D. / Forsgren, N. / Akfur, C. / Allgardsson, A. / Qian, W. / Engdahl, C. / Berg, L. / 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
DepositionJun 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 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 1.4Dec 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 1.5Oct 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)129,35625
Polymers119,5292
Non-polymers9,82723
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-15.9 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.671, 110.824, 227.112
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, 6 molecules AB

#1: Protein ACETYLCHOLINESTERASE / ACHE


Mass: 59764.488 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
#3: 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.: 4
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, 337 molecules

#2: Chemical
ChemComp-5GZ / 4-(2-chloro-6-nitrophenoxy)-N-[2-(diethylamino)ethyl]benzenesulfonamide


Mass: 427.902 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H22ClN3O5S
#4: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C28H58O15
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 41 % / 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: 0.9805
DetectorDetector: CCD / Date: Jan 13, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9805 Å / Relative weight: 1
ReflectionResolution: 2.5→29.05 Å / Num. obs: 69367 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 44.02 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

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Processing

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

1j06


Resolution: 2.5→28.813 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
Details: RESIDUES 258-264 WERE EXCLUDED FROM THE MODEL DUE TO LACK OF ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.2316 1384 2 %
Rwork0.1908 --
obs0.1916 68722 98.86 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.932 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 55.01 Å2
Baniso -1Baniso -2Baniso -3
1-3.4814 Å20 Å20 Å2
2--14.3665 Å20 Å2
3----17.848 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 263 318 8906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078896
X-RAY DIFFRACTIONf_angle_d1.09412115
X-RAY DIFFRACTIONf_dihedral_angle_d16.6673284
X-RAY DIFFRACTIONf_chiral_restr0.0771287
X-RAY DIFFRACTIONf_plane_restr0.0051576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.33571460.28186608X-RAY DIFFRACTION99
2.5893-2.69290.32421490.2626636X-RAY DIFFRACTION99
2.6929-2.81540.31310.26016678X-RAY DIFFRACTION99
2.8154-2.96370.27141360.22796640X-RAY DIFFRACTION99
2.9637-3.14910.26721540.22356678X-RAY DIFFRACTION99
3.1491-3.39190.28041150.22316735X-RAY DIFFRACTION99
3.3919-3.73260.24351490.19926730X-RAY DIFFRACTION99
3.7326-4.27120.21621330.15816724X-RAY DIFFRACTION98
4.2712-5.37560.15591310.1446816X-RAY DIFFRACTION99
5.3756-28.81480.19881400.17127093X-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)
13.3564-1.04570.02562.0142-0.55394.4758-0.1963-0.19740.15230.4640.18630.04260.0118-0.3499-0.01560.3575-0.0103-0.02760.43220.01130.201229.686312.806341.3651
20.6208-0.1488-0.04420.8516-0.24251.8128-0.1776-0.60560.28550.23920.1372-0.2683-0.00880.01080.03870.316-0.0161-0.04270.5378-0.0170.086533.237617.436729.1879
32.1202-0.0705-0.98031.5108-0.02934.5819-0.0502-0.1429-0.12370.23060.0164-0.10820.23840.02220.03880.29520.0105-0.07290.350.02640.191531.68039.145225.3053
41.92080.1204-1.99551.4543-0.69116.1995-0.0358-0.2937-0.15780.12650.06620.01470.4601-0.4187-0.01290.2836-0.0193-0.03180.25720.03960.14227.56872.301718.206
54.19211.17285.02931.35811.55966.0583-0.18290.3811-0.0458-0.2684-0.1169-0.316-0.24381.01550.27670.28070.06270.0270.78310.08170.271853.65913.030211.9151
62.88942.0111.00235.33970.95423.46070.00930.2888-0.06270.28490.0011-0.3040.19710.3429-0.01020.25420.09050.0210.53540.03930.211440.023711.19039.2738
72.78040.9321-0.78615.3657-2.06434.0594-0.07190.35930.04070.0632-0.0150.0207-0.0323-0.21590.09660.1415-0.0412-0.0020.32550.01510.170223.835817.79762.7978
82.3497-2.1991-0.02374.48920.2872.17510.19640.59590.1494-0.3755-0.18410.11240.19950.0823-0.04830.291-0.03840.00050.57220.03820.176922.905817.7599-8.454
91.61170.23520.2523.89910.92122.9673-0.03190.0960.03870.03430.05020.33030.0822-0.7082-0.020.2162-0.0312-0.01430.58770.040.199614.274413.626616.1449
103.8904-1.2593-1.37688.5862-1.09782.2005-0.19280.1179-0.80770.1903-0.01121.19030.5189-1.39490.20810.3491-0.21090.00540.87080.05350.43866.95151.024913.4346
111.6128-0.4651-1.59471.90240.9715.7747-0.0643-0.0693-0.0767-0.5329-0.09580.35820.54510.1252-0.00780.353-0.039-0.2290.94030.00360.137317.61216.0928-1.3185
122.5209-0.24510.66911.9497-0.24344.60810.21280.60370.1243-0.3903-0.19920.2829-0.2285-0.8365-0.0160.38830.032-0.0840.668-0.13210.2274-3.726.2561-61.8018
130.5961-0.43110.54521.46610.23542.14160.30750.3687-0.1366-0.165-0.26860.12510.8846-0.0882-0.10830.5816-0.0786-0.09980.6655-0.13220.24965.3722-4.1337-53.1468
141.49670.20030.05041.30720.6662.7230.04710.3549-0.1714-0.2539-0.13920.15030.1874-0.19150.03210.34060.0171-0.06560.5852-0.07760.13754.10674.1348-51.072
151.0428-0.3647-0.02361.63830.89923.06520.08190.0437-0.0903-0.03150.0839-0.1370.29020.3901-0.16040.30680.0369-0.05140.5758-0.06050.177416.55123.0263-47.4148
162.349-1.5951-0.59912.2175-0.07774.9620.19470.23820.24690.0636-0.0659-0.2586-0.08370.4682-0.13750.2215-0.0578-0.07460.4106-0.0560.143515.044710.6142-36.8734
173.9031.21480.641.94130.27215.60790.2206-0.8224-0.27220.4139-0.0307-0.02850.90590.0979-0.15770.64230.0074-0.11540.40290.00050.248414.2142-5.304-18.5396
181.1420.7659-0.26684.22930.35823.51510.039-0.0222-0.03690.1103-0.03870.25650.1963-0.3665-0.00720.28720.0060.00120.582-0.07640.2036-2.42398.3091-33.3972
193.42871.40331.5617.9371-2.74972.66020.0276-0.50270.64040.49430.37910.9116-0.4337-1.0682-0.37720.42290.08910.07610.7462-0.04910.3008-0.988822.2256-28.8968
201.70410.10262.97991.87-0.11085.25630.2122-0.1128-0.15860.2656-0.22140.15440.17650.61880.08230.4628-0.0568-0.00420.7597-0.0572-0.015313.27811.2396-21.7828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:45)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 46:111)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 112:190)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 191:240)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 241:275)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 276:318)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 319:366)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 367:406)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 407:486)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 487:513)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 514:542)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 4:45)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 46:86)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 87:170)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 171:300)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 301:341)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 342:406)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 407:486)
19X-RAY DIFFRACTION19CHAIN B AND (RESSEQ 487:513)
20X-RAY DIFFRACTION20CHAIN B AND (RESSEQ 514:543)

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