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- PDB-4arb: Mus musculus Acetylcholinesterase in complex with (S)-C5685 at 2.... -

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Basic information

Entry
Database: PDB / ID: 4arb
TitleMus musculus Acetylcholinesterase in complex with (S)-C5685 at 2.25 A resolution.
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ENATIOMERS / INHIBITOR / CHEMICAL LEAD
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 / side of membrane / laminin binding / 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-C57 / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBerg, L. / Niemiec, M.S. / Qian, W. / Andersson, C.D. / WittungStafshede, P. / Ekstrom, F. / Linusson, A.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Similar But Different: Thermodynamic and Structural Characterization of a Pair of Enantiomers Binding to Acetylcholinesterase.
Authors: Berg, L. / Niemiec, M.S. / Qian, W. / Andersson, C.D. / Wittung-Stafshede, P. / Ekstrom, F. / Linusson, A.
#1: Journal: Plos One / Year: 2011
Title: Targeting Acetylcholinesterase: Identification of Chemical Leads by High Throughput Screening, Structure Determination and Molecular Modeling.
Authors: Berg, L. / Andersson, C.D. / Artursson, E. / Hornberg, A. / Tunemalm, A. / Linusson, A. / Ekstrom, F.
History
DepositionApr 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / atom_site_anisotrop / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.1Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 2.2Jul 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 2.3Dec 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
Revision 2.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)122,75114
Polymers120,4682
Non-polymers2,28412
Water17,817989
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-4.3 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.926, 111.781, 227.071
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) / Cell line (production host): HEK293F / 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 , 4 types, 998 molecules

#2: Chemical ChemComp-C57 / 4-(DIMETHYLAMINO)-N-{[(2S)-1-ETHYLPYRROLIDIN-2-YL]METHYL}-2-METHOXY-5-NITROBENZAMIDE


Mass: 350.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N4O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details4-(DIMETHYLAMINO)-N-{[(2R)-1-ETHYLPYRROLIDIN- 2-YL]METHYL}-2-METHOXY-5-NITROBENZAMIDE (568): ...4-(DIMETHYLAMINO)-N-{[(2R)-1-ETHYLPYRROLIDIN- 2-YL]METHYL}-2-METHOXY-5-NITROBENZAMIDE (568): CORRESPONDING TO LIGAND C57 IN THE RACEMIC STRUCTURE 4A23

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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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES, 30 % (V/V) POLYETHELENEGLYCOLEMONOMETHYLETHER, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.039
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 29, 2011 / Details: MIRRORS
RadiationMonochromator: RH-COATED SI MIRROR, BENT FOR VERTICAL COLLIMATION
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.25→29.1 Å / Num. obs: 96077 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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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: 2.25→28.806 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1893 2 %
Rwork0.1715 --
obs0.1722 95904 99.89 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.323 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3384 Å20 Å20 Å2
2--2.5156 Å20 Å2
3----3.8539 Å2
Refinement stepCycle: LAST / Resolution: 2.25→28.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8295 0 153 989 9437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088776
X-RAY DIFFRACTIONf_angle_d1.0911969
X-RAY DIFFRACTIONf_dihedral_angle_d16.6643166
X-RAY DIFFRACTIONf_chiral_restr0.0781284
X-RAY DIFFRACTIONf_plane_restr0.0051571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30630.32421310.25996602X-RAY DIFFRACTION100
2.3063-2.36860.29711340.24396643X-RAY DIFFRACTION100
2.3686-2.43820.2771330.22876642X-RAY DIFFRACTION100
2.4382-2.51690.25711190.21916652X-RAY DIFFRACTION100
2.5169-2.60680.26331380.20156676X-RAY DIFFRACTION100
2.6068-2.71110.27341500.20066664X-RAY DIFFRACTION100
2.7111-2.83440.2371380.20256650X-RAY DIFFRACTION100
2.8344-2.98370.23431330.18086704X-RAY DIFFRACTION100
2.9837-3.17040.21061530.17526685X-RAY DIFFRACTION100
3.1704-3.41480.21241150.18046729X-RAY DIFFRACTION100
3.4148-3.75780.1971480.16276713X-RAY DIFFRACTION100
3.7578-4.30.1771310.13546779X-RAY DIFFRACTION100
4.3-5.41170.14951330.12886819X-RAY DIFFRACTION100
5.4117-28.80810.20161370.17427053X-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)
10.23910.0017-0.06940.175-0.04831.0047-0.0438-0.08810.02540.07190.0221-0.04430.05160.042100.26460.0076-0.01120.23970.03230.273631.208811.299128.9999
21.01840.2585-0.10560.0643-0.47971.2735-0.08910.213-0.089-0.0831-0.0196-0.08170.23890.257900.26420.04140.01940.23480.01990.316540.52219.931510.2869
30.4685-0.05060.25120.3454-0.24811.8033-0.03210.09050.0152-0.08090.00740.08650.0158-0.266700.2307-0.0206-0.00720.25950.02040.287518.706517.42416.4363
40.1025-0.11970.13170.198-0.09170.1138-0.04520.198-0.1113-0.10380.09380.50210.6675-0.89450.00040.3952-0.1935-0.01180.53630.04670.44446.93591.338313.5125
50.2836-0.1560.4453-0.0757-0.130.52310.1991-0.01530.0005-0.2693-0.13430.2499-0.06380.047100.3523-0.0561-0.0580.428-0.00340.38417.28546.3249-1.0277
60.247-0.00830.31970.4960.14350.7685-0.02890.2933-0.021-0.2022-0.0718-0.0605-0.0268-0.2764-00.30310.0569-0.06690.4555-0.0760.3374-3.62096.1949-61.79
7-0.14480.0640.15850.43530.1880.42770.05510.2136-0.1023-0.0542-0.07980.02050.25820.033100.4212-0.001-0.04080.4162-0.08150.33775.2144-4.2019-52.952
80.19280.22550.44070.36260.26711.41110.04770.1461-0.1781-0.0732-0.04850.05620.1067-0.1163-00.26920.0047-0.03640.3304-0.06590.28323.91774.0898-50.9208
90.26090.0051-0.3360.25790.2790.4760.02970.108-0.0077-0.02680.02970.0254-0.14210.045500.31950.0167-0.01620.3344-0.02990.30069.194913.3797-48.2655
100.2473-0.23450.2420.4135-0.10410.21470.08130.1012-0.05850.20570.0516-0.1090.35950.600600.4050.1291-0.09190.4446-0.07480.368324.0118-8.3606-45.956
110.6304-0.39740.18290.53180.62521.12690.07420.02640.06740.04710.009-0.04980.02640.1718-0.00010.2984-0.039-0.03150.2801-0.05760.334314.886310.7038-36.7752
120.47610.01220.29870.22690.43911.51450.1166-0.0545-0.00720.184-0.11110.05910.2369-0.126-00.3423-0.05-0.01110.2729-0.02310.30894.60172.4875-26.6503
130.1251-0.0622-0.22610.23060.1440.36560.0779-0.19330.5080.1458-0.06330.3032-0.2831-0.1344-0.00020.33920.01120.00350.2581-0.0540.3472-1.403422.5491-28.6421
140.06240.00850.22490.0994-0.01750.59350.1209-0.0032-0.08570.0694-0.1010.1504-0.01210.1605-00.35790.0065-0.00140.4036-0.01930.296613.169611.3791-21.5857
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 46:86)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 87:170)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 171:237)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 238:300)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 301:341)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 342:486)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 487:513)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 514:543)

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