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- PDB-4b7z: Mus musculus Acetylcholinesterase in complex with N-(2-Diethylami... -

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Basic information

Entry
Database: PDB / ID: 4b7z
TitleMus musculus Acetylcholinesterase in complex with N-(2-Diethylamino-ethyl)-1-(4-methylphenyl)-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
DI(HYDROXYETHYL)ETHER / Chem-Q4Q / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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: 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 1.5Dec 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

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,55423
Polymers120,4682
Non-polymers3,08621
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-36.6 kcal/mol
Surface area38240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.307, 111.833, 226.738
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 , 5 types, 766 molecules

#2: Chemical ChemComp-Q4Q / N-[2-(diethylamino)ethyl]-1-(4-methylphenyl)methanesulfonamide


Mass: 284.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N2O2S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#4: 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
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 748 / 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: 27-30% (V/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: 2.3→29.12 Å / Num. obs: 90383 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Biso Wilson estimate: 42.97 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.3 / % possible all: 99.7

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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: 2.3→28.797 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML
Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED: CHAIN A 258-264 AND 543-548, CHAIN B 1-3, 258-264 AND 544-548. DUE TO INSUFFICIENT ELECTRON DENSITY THE ...Details: DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE NOT MODELED: CHAIN A 258-264 AND 543-548, CHAIN B 1-3, 258-264 AND 544-548. DUE TO INSUFFICIENT ELECTRON DENSITY THE FOLLOWING RESIDUES WERE MODELED AS ALANINES, CHAIN A 496 AND CHAIN B 493.
RfactorNum. reflection% reflection
Rfree0.2006 1784 2 %
Rwork0.1711 --
obs0.1717 90244 99.9 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.03 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 46.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.332 Å20 Å20 Å2
2--3.0582 Å20 Å2
3----1.7261 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 200 748 9284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088784
X-RAY DIFFRACTIONf_angle_d1.08611948
X-RAY DIFFRACTIONf_dihedral_angle_d17.8683214
X-RAY DIFFRACTIONf_chiral_restr0.0771277
X-RAY DIFFRACTIONf_plane_restr0.0051553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.25541440.22966744X-RAY DIFFRACTION100
2.3622-2.43160.27861300.22766716X-RAY DIFFRACTION100
2.4316-2.51010.21561180.21836724X-RAY DIFFRACTION100
2.5101-2.59970.27961450.21726744X-RAY DIFFRACTION100
2.5997-2.70380.28711490.21726706X-RAY DIFFRACTION100
2.7038-2.82670.22181350.19746778X-RAY DIFFRACTION100
2.8267-2.97560.20971380.17616765X-RAY DIFFRACTION100
2.9756-3.16180.18341500.16916761X-RAY DIFFRACTION100
3.1618-3.40560.19131200.17146811X-RAY DIFFRACTION100
3.4056-3.74760.21231470.15796813X-RAY DIFFRACTION100
3.7476-4.28840.18181350.14016862X-RAY DIFFRACTION100
4.2884-5.39710.15671340.13796923X-RAY DIFFRACTION100
5.3971-28.7990.1891390.18347113X-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)
10.5765-0.0988-0.13031.0172-0.21032.7638-0.0227-0.1189-0.01070.12190.0154-0.03870.13990.08280.01340.1901-0.0062-0.01120.18020.03960.210330.795311.54229.366
23.50450.84680.29061.065-0.35232.3764-0.06190.1696-0.2285-0.0796-0.0287-0.22350.3030.39270.07450.26030.05890.03760.23750.01410.245139.94139.805410.502
31.12710.06420.10041.2134-0.45783.177-0.0290.07740.0006-0.09260.02740.16070.0393-0.3399-0.00670.1499-0.0274-0.02610.22830.01530.245818.319817.63876.651
45.3860.01881.38768.478-3.01323.04910.0011-0.1832-0.35060.40390.13230.87980.5221-1.3913-0.04760.3242-0.2027-0.02070.59710.04870.446.30521.673414.7315
52.5603-0.9867-2.17682.20880.93954.95920.01920.1009-0.1719-0.1237-0.14840.27180.5139-0.28470.090.2341-0.0897-0.10030.2995-0.00880.221417.09616.6215-0.7443
64.5521-0.9053-0.98672.53650.33094.62840.04240.57620.125-0.4695-0.10780.4213-0.2929-0.6604-0.00570.26670.0416-0.11730.2695-0.10770.2672-3.80345.9812-61.6916
70.9556-0.0017-0.12771.02020.5182.47130.08220.191-0.1725-0.1562-0.04730.17730.2938-0.2141-0.03780.2852-0.0282-0.06070.3123-0.09270.30722.24471.1306-51.2632
81.4414-0.63250.01512.22280.75042.47880.07570.1870.0274-0.00720.0217-0.23650.08960.4016-0.09660.1713-0.0199-0.02710.274-0.04370.223617.09925.3621-45.851
91.4315-0.19630.65321.6101-0.09282.71910.1605-0.136-0.15790.2645-0.09040.13470.4062-0.1922-0.08830.3665-0.05020.01240.2459-0.05370.30834.32962.1532-26.6972
104.85040.92711.34014.9483-1.52989.384-0.0069-0.28830.76930.23730.12670.7816-0.7455-0.5105-0.07540.35820.0370.04850.2444-0.0530.4185-1.711622.3636-28.5929
117.01290.00594.49692.0649-0.19463.92960.23230.227-0.18090.2045-0.1174-0.00320.08890.3944-0.08580.3801-0.03980.02510.2832-0.03120.181312.73711.3756-21.3522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:228)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 229:331)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 332:486)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 487:513)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 514:542)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 4:45)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 46:158)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 159:331)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 332:486)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 487:513)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 514:543)

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