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- PDB-5ehn: mAChE-syn TZ2PA5 complex -

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Basic information

Entry
Database: PDB / ID: 5ehn
TitlemAChE-syn TZ2PA5 complex
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / inhibitor / click chemistry / triazole
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 / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / 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-5NZ / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBourne, Y. / Marchot, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Steric and Dynamic Parameters Influencing In Situ Cycloadditions to Form Triazole Inhibitors with Crystalline Acetylcholinesterase.
Authors: Bourne, Y. / Sharpless, K.B. / Taylor, P. / Marchot, P.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: 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

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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)121,3286
Polymers119,5292
Non-polymers1,7994
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-3 kcal/mol
Surface area37690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.750, 112.450, 227.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 59764.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P21836, 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-5NZ / 6-phenyl-5-[5-[3-[2-(1,2,3,4-tetrahydroacridin-9-ylamino)ethyl]-1,2,3-triazol-4-yl]pentyl]phenanthridin-5-ium-3,8-diamine


Mass: 647.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H43N8
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25-35%PEG550 MME or PEG600, 60-100 mM sodium acetate
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 62667 / % possible obs: 98.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 60.93 Å2 / Rsym value: 0.069 / Net I/σ(I): 18.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j06

1j06


Resolution: 2.6→45 Å / Cor.coef. Fo:Fc: 0.9195 / Cor.coef. Fo:Fc free: 0.9134 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.197
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 1268 2.02 %RANDOM
Rwork0.1816 ---
obs0.1821 62667 98.46 %-
Displacement parametersBiso mean: 52.47 Å2
Baniso -1Baniso -2Baniso -3
1--9.8399 Å20 Å20 Å2
2---10.5334 Å20 Å2
3---20.3733 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: 1 / Resolution: 2.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8340 0 131 214 8685
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018742HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.111958HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2844SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes188HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1290HARMONIC5
X-RAY DIFFRACTIONt_it8742HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion17.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1063SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10057SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2491 114 2.47 %
Rwork0.2183 4506 -
all0.2191 4620 -
obs--99.5 %
Refinement TLS params.

S31: 0.2023 Å ° / 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 °)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)
10.83960.03930.18540.7578-0.3682.0054-0.07320.0005-0.0386-0.02360.00830.0162-0.09970.0649-0.05230.02260.0076-0.10340.0295-0.121827.961212.541616.7877
20.81790.02640.09711.26490.70622.30830.09980.0785-0.07050.1353-0.12870.1237-0.02560.0289-0.1029-0.0317-0.0076-0.0988-0.0714-0.15957.80174.3649-40.251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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