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- PDB-5eih: mAChE-TZ2/PA5 complex -

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Basic information

Entry
Database: PDB / ID: 5eih
TitlemAChE-TZ2/PA5 complex
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / inhibitor / click chemistry / peripheral anionic site
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / laminin binding / collagen 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, 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
ACETATE ION / Chem-PZ5 / Chem-TZ2 / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Jan 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)120,8458
Polymers119,5292
Non-polymers1,3166
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-10 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.500, 112.978, 226.504
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 , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 223 molecules

#2: Chemical ChemComp-TZ2 / ~{N}-(2-azidoethyl)-1,2,3,4-tetrahydroacridin-9-amine


Mass: 267.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5
#3: Chemical ChemComp-PZ5 / 5-hept-6-ynyl-6-phenyl-phenanthridin-5-ium-3,8-diamine


Mass: 380.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 217 / 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

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25-35% PEG MME 550 or PEG 600, 60-100 mM Hepes or sodium acetate
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.7→46 Å / Num. obs: 56558 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 60.89 Å2 / Rsym value: 0.113 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4

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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: 2.7→46 Å / Cor.coef. Fo:Fc: 0.9166 / Cor.coef. Fo:Fc free: 0.8951 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.296 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1153 2.04 %RANDOM
Rwork0.1746 ---
obs0.1751 56558 99.41 %-
Displacement parametersBiso mean: 50.75 Å2
Baniso -1Baniso -2Baniso -3
1--11.6378 Å20 Å20 Å2
2---9.0647 Å20 Å2
3---20.7025 Å2
Refine analyzeLuzzati coordinate error obs: 0.311 Å
Refinement stepCycle: 1 / Resolution: 2.7→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8410 0 96 217 8723
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018773HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1111994HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2860SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes192HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1305HARMONIC5
X-RAY DIFFRACTIONt_it8773HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion18.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1066SEMIHARMONIC5
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_contact10397SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2594 74 1.8 %
Rwork0.2137 4048 -
all0.2145 4122 -
obs--99.2 %
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)
10.9754-0.10990.2210.9126-0.35442.2033-0.08880.0185-0.0376-0.04110.00510.02690.2059-0.06550.0837-0.08980.00520.0072-0.10310.0387-0.119127.84612.5316.6471
20.8701-0.01640.19261.29830.77952.67210.13580.0977-0.06140.1367-0.17780.1090.2295-0.03970.042-0.1264-0.0184-0.018-0.0931-0.0827-0.16727.80874.7511-40.1837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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