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

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Basic information

Entry
Database: PDB / ID: 4ara
TitleMus musculus Acetylcholinesterase in complex with (R)-C5685 at 2.5 A resolution.
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / ENATIOMERS / INHIBITOR / CHEMICAL LEAD
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-C56 / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 20, 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)123,55826
Polymers120,4682
Non-polymers3,09024
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-14.2 kcal/mol
Surface area38240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.764, 112.012, 227.340
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
#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 , 6 types, 649 molecules

#2: Chemical ChemComp-C56 / 4-(DIMETHYLAMINO)-N-{[(2R)-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.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details4-(DIMETHYLAMINO)-N-{[(2S)-1-ETHYLPYRROLIDIN- 2-YL]METHYL}-2-METHOXY-5-NITROBENZAMIDE (568): ...4-(DIMETHYLAMINO)-N-{[(2S)-1-ETHYLPYRROLIDIN- 2-YL]METHYL}-2-METHOXY-5-NITROBENZAMIDE (568): CORRESPONDING TO LIGAND C56 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: I911-5 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2012 / 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 Å / Relative weight: 1
ReflectionResolution: 2.5→28.98 Å / Num. obs: 70472 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Biso Wilson estimate: 39.74 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4 / % possible all: 100

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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→28.855 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1416 2 %
Rwork0.1826 --
obs0.1834 70252 99.79 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.44 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.8219 Å20 Å20 Å2
2--12.843 Å20 Å2
3----23.6649 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8294 0 204 628 9126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048837
X-RAY DIFFRACTIONf_angle_d0.89812028
X-RAY DIFFRACTIONf_dihedral_angle_d15.7643242
X-RAY DIFFRACTIONf_chiral_restr0.0621284
X-RAY DIFFRACTIONf_plane_restr0.0051569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.30721540.25166772X-RAY DIFFRACTION100
2.5893-2.69290.29131540.22836773X-RAY DIFFRACTION100
2.6929-2.81540.25211340.21886819X-RAY DIFFRACTION100
2.8154-2.96370.27631360.20176822X-RAY DIFFRACTION100
2.9637-3.14920.22511520.20386812X-RAY DIFFRACTION100
3.1492-3.3920.26111300.20516883X-RAY DIFFRACTION100
3.392-3.73270.22111410.18366867X-RAY DIFFRACTION100
3.7327-4.27130.18681400.14966914X-RAY DIFFRACTION100
4.2713-5.37570.16231320.14056985X-RAY DIFFRACTION100
5.3757-28.8570.21641430.18857189X-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)
10.1653-0.0646-0.00230.1515-0.03621.1039-0.0523-0.09820.03480.12470.0154-0.0733-0.06590.0513-00.2680.0043-0.00620.23770.02160.273330.333115.422732.1785
20.14830.22770.36330.59670.14290.815-0.0073-0.049-0.02780.11010.0576-0.04610.19220.023400.28880.0377-0.00430.19610.04190.278733.24784.120224.0344
30.80010.32290.22840-0.39811.322-0.08840.13770.0056-0.03130.0118-0.00870.17420.1599-0.00020.16220.04290.03190.12450.01920.221737.791910.901910.3854
40.2268-0.07970.35790.50330.14151.4203-0.03420.11240.0048-0.11210.03270.08350.0444-0.2615-00.1834-0.0244-0.00650.24240.0320.261918.522917.17416.3422
50.2896-0.2812-0.13980.33840.04460.8203-0.0970.4955-0.1487-0.0701-0.00420.56850.3724-1.06540.00120.3515-0.29530.01340.4830.07650.41916.871.464913.7085
60.0313-0.00930.14620.009-0.04420.65340.0674-0.15760.0765-0.3743-0.0490.17120.24590.20760.00940.266-0.0665-0.04760.462-0.01640.271117.6556.3933-1.143
70.1856-0.10660.27670.7024-0.01680.90430.07470.3060.0863-0.3115-0.13660.0126-0.1399-0.3327-0.00080.2640.0732-0.08240.4445-0.08490.3153-3.63576.1103-61.5447
8-0.0538-0.0542-0.16480.5770.45340.53590.07810.2434-0.0439-0.1155-0.16930.03860.54950.0695-0.00740.3597-0.0442-0.03130.3593-0.06290.31435.289-4.2856-52.9246
90.55360.3230.22680.16220.14610.60060.03920.1752-0.1582-0.2557-0.21720.08250.3045-0.4991-0.0120.19610.0221-0.08820.3488-0.08810.2721-1.3094.6399-50.3098
100.12820.1347-0.03860.1281-0.03790.72860.15920.324-0.113-0.2351-0.08860.0934-0.12630.22060.00010.30990.0174-0.03220.3635-0.06480.286112.31056.7368-54.0317
110.0075-0.18660.06360.27160.29670.9570.0677-0.0016-0.04850.02360.0025-0.0339-0.07710.21050.00010.22670.0043-0.03050.3075-0.03260.264315.17988.2124-44.1651
120.2412-0.25690.10660.25350.03650.13560.06220.0922-0.16810.0286-0.0414-0.02180.35120.5162-0.00010.42270.1473-0.09210.3671-0.07780.321522.4756-9.8867-46.813
130.4274-0.29920.09640.30050.25160.7741-0.10140.24860.12850.00670.1129-0.0960.02920.3509-0.00010.1739-0.0455-0.02190.2684-0.03790.272818.287614.2963-40.1912
140.16830.068-0.07020.34010.09060.28210.129-0.12090.00460.22110.0258-0.02450.56190.22450.00060.55380.0191-0.03610.2004-0.00320.337713.8485-6.1946-22.0912
150.14480.3314-0.12320.64580.33011.4030.1272-0.09050.04180.187-0.16250.03170.0814-0.1277-00.1865-0.0454-0.00480.2232-0.03580.22590.73525.836-29.0308
160.1012-0.0023-0.19590.1330.07120.37250.0429-0.5460.25980.0021-0.01910.3205-0.3827-0.41710.0010.37330.0523-0.01910.349-0.05930.3594-1.050322.4945-28.6338
17-0.0023-0.02120.0037-0.0104-0.09130.4414-0.03360.0358-0.03560.1517-0.02240.15430.09370.2484-00.39-0.0125-0.00430.4073-0.05390.250213.357311.4043-21.5981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:142)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 143:223)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 224:341)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 342:486)
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 46:86)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 87:142)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 143:190)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 191:255)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 256:297)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 298:331)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 332:382)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 383:486)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 487:513)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 514:543)

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