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- PDB-5foq: Acetylcholinesterase in complex with C7653 -

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Basic information

Entry
Database: PDB / ID: 5foq
TitleAcetylcholinesterase in complex with C7653
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / SIGNALING PROTEIN / QUANTUM CHEMISTRY / DENSITY FUNCTIONAL THEORY / DRUG DESIGN
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nuclear envelope / presynaptic membrane / positive regulation of cold-induced thermogenesis / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / 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 / Alpha/Beta hydrolase fold, catalytic domain ...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-GC8 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / Acetylcholinesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBerg, L. / Mishra, B.K. / Andersson, D.C. / Ekstrom, F. / Linusson, A.
CitationJournal: Chemistry / Year: 2016
Title: The Nature of Activated Non-Classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes.
Authors: Berg, L. / Mishra, B.K. / Andersson, C.D. / Ekstrom, F. / Linusson, A.
History
DepositionNov 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Source and taxonomy
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jul 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 2.2May 12, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 2.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)122,69512
Polymers120,4682
Non-polymers2,22710
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint21 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.020, 111.770, 227.090
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


Mass: 60233.984 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, 1-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: HOMO SAPIENS (human) / References: UniProt: P21836*PLUS, acetylcholinesterase
#2: 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, 302 molecules

#3: Chemical ChemComp-GC8 / 2-(2,4-dichlorophenoxy)-N-[4-(1-piperidinylmethyl)phenyl]acetamide


Mass: 393.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22Cl2N2O2
#4: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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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: 4.16 Å3/Da / Density % sol: 70.45 % / Description: NONE
Crystal growpH: 7 / Details: PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.3→29.7 Å / Num. obs: 89319 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 43.62 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.1 / % possible all: 96.4

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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: 2.3→28.978 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1746 2 %
Rwork0.1915 --
obs0.1922 88553 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→28.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8316 0 146 295 8757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088740
X-RAY DIFFRACTIONf_angle_d1.06911920
X-RAY DIFFRACTIONf_dihedral_angle_d15.9073155
X-RAY DIFFRACTIONf_chiral_restr0.0731281
X-RAY DIFFRACTIONf_plane_restr0.0051557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.42391360.34716876X-RAY DIFFRACTION95
2.3677-2.4440.35441340.30877002X-RAY DIFFRACTION96
2.444-2.53130.31871380.27267097X-RAY DIFFRACTION97
2.5313-2.63260.25281500.23967172X-RAY DIFFRACTION98
2.6326-2.75240.27951520.22517196X-RAY DIFFRACTION99
2.7524-2.89730.28751550.22777249X-RAY DIFFRACTION99
2.8973-3.07870.25791550.22977256X-RAY DIFFRACTION99
3.0787-3.31610.27951460.22177310X-RAY DIFFRACTION99
3.3161-3.64920.23891360.19587259X-RAY DIFFRACTION99
3.6492-4.17590.19231410.16457301X-RAY DIFFRACTION98
4.1759-5.25610.14051470.13887392X-RAY DIFFRACTION99
5.2561-28.98060.17861560.16127697X-RAY DIFFRACTION100
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)
11.2634-0.3036-0.53561.6238-0.75032.8461-0.1389-0.25850.08080.2820.0868-0.0073-0.13130.0560.05160.3427-0.0027-0.04360.2925-0.02640.270533.207916.290733.6435
23.73660.3921-2.14971.13480.12833.7096-0.0771-0.38-0.00080.17780.0488-0.02070.24440.13930.0430.28760.0255-0.04760.25820.06730.212130.666612.655326.7371
32.1681-0.3845-0.33960.92861.14652.3772-0.0857-0.1985-0.29640.17150.13530.01790.5206-0.2561-0.07810.36820.0120.00710.23540.08590.297929.53142.837626.3217
43.36710.27310.15121.1694-0.28623.0252-0.05390.2098-0.2941-0.0879-0.0434-0.16870.40670.2650.11270.30540.08260.02030.2210.01820.262339.97358.364411.5652
51.42240.0278-0.28692.9652-1.32613.38640.0640.27370.0552-0.1377-0.09730.1068-0.0236-0.11260.01880.2753-0.0076-0.02920.36090.03490.288623.3620.0854-3.5902
62.2568-0.1796-0.2062.83580.40853.6091-0.0347-0.0717-0.1058-0.01180.05580.36430.1286-0.67-0.03770.201-0.0545-0.02520.38870.03610.324814.396113.780316.3594
74.3630.79191.16347.4416-3.01534.486-0.0098-0.0514-0.43950.2420.24450.67560.452-1.5197-0.17490.4361-0.229-0.00280.58420.08680.47556.90611.166514.2887
82.5591-1.1333-2.31082.98122.52559.3460.0305-0.155-0.0152-0.3874-0.05720.30310.33220.21680.15640.3721-0.0631-0.12020.3590.02480.296617.62336.0635-1.14
92.1254-0.1555-1.17981.7971-0.29554.25350.14840.73170.0708-0.3574-0.16180.2863-0.2538-0.90770.0430.43830.0493-0.11480.5968-0.16110.3801-3.85816.1165-61.599
101.1158-0.35210.27191.47390.5363.59720.11310.2416-0.2234-0.1306-0.14540.27260.4705-0.33440.01940.368-0.0198-0.06230.4443-0.1160.3352.35881.1284-51.4004
117.5839-4.59061.81094.4122-1.52673.26260.50220.5129-0.2299-0.478-0.30420.0559-0.18350.1995-0.19470.36550.0288-0.00630.4904-0.09320.31413.96728.5866-55.3622
121.7497-0.85070.0422.3110.7253.17320.16290.1127-0.18120.09540.0133-0.18130.32590.4808-0.17050.30290.0425-0.04690.4169-0.07480.273517.69411.5193-45.1846
135.1651-1.7018-2.32621.4211.83635.06370.26370.36990.6489-0.02460.1067-0.3611-0.23820.5934-0.35910.3231-0.0418-0.05840.4333-0.05170.350518.258414.1798-40.0425
141.8521-0.20860.74631.41960.23092.75330.1788-0.1291-0.28990.2358-0.09420.19430.4827-0.2216-0.09890.3956-0.07080.01980.3329-0.07040.30814.75021.9736-26.7863
157.59062.06461.6214.5257-1.33057.73070.0032-0.41730.7768-0.06770.04090.389-0.029-0.68760.00340.37330.0347-0.01740.3291-0.08640.3072-1.063322.3808-28.7326
168.54-0.64493.13532.1492-0.12884.70.1485-0.1843-0.26810.097-0.079-0.0410.01360.6292-0.08770.4374-0.07030.01380.4403-0.0210.226313.309311.3368-21.5192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 86 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 87 THROUGH 170 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 171 THROUGH 214 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 215 THROUGH 324 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 325 THROUGH 406 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 407 THROUGH 486 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 487 THROUGH 513 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 514 THROUGH 542 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 4 THROUGH 45 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 46 THROUGH 158 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 159 THROUGH 190 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 191 THROUGH 297 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 298 THROUGH 331 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 332 THROUGH 486 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 487 THROUGH 513 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 514 THROUGH 543 )

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