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- PDB-5dtj: Crystal Structure of dfp-inhibited mouse acetylcholinesterase in ... -

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Basic information

Entry
Database: PDB / ID: 5dtj
TitleCrystal Structure of dfp-inhibited mouse acetylcholinesterase in complex with the reactivator SP-134
ComponentsAcetylcholinesterase
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor complex
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
1-[5-(2,4-dichlorophenoxy)pentyl]-1H-imidazole / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsTran, T.H. / Tong, L.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)N000141110900 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)5R21NS08079002 United States
National Institutes of Health/Office of the Director1S10OD01812101 United States
CitationJournal: Chembiochem / Year: 2015
Title: Discovery of New Classes of Compounds that Reactivate Acetylcholinesterase Inhibited by Organophosphates.
Authors: Katz, F.S. / Pecic, S. / Tran, T.H. / Trakht, I. / Schneider, L. / Zhu, Z. / Ton-That, L. / Luzac, M. / Zlatanic, V. / Damera, S. / Macdonald, J. / Landry, D.W. / Tong, L. / Stojanovic, M.N.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Source and taxonomy
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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)121,4546
Polymers120,2582
Non-polymers1,1974
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.487, 113.367, 227.117
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: 60128.840 Da / Num. of mol.: 2 / Fragment: UNP residues 32-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell (production host): Hi-5 insect cells by C-PERL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P21836, acetylcholinesterase
#2: Chemical
ChemComp-5G8 / 1-[5-(2,4-dichlorophenoxy)pentyl]-1H-imidazole


Mass: 299.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16Cl2N2O

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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: 4.25 Å3/Da / Density % sol: 71.09 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% v/v PEG 600, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 56474 / % possible obs: 100 % / Redundancy: 5.5 % / Net I/σ(I): 16.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HA2

2ha2


Resolution: 2.71→46.202 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 1996 3.55 %
Rwork0.1786 --
obs0.1801 56292 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→46.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8373 0 66 0 8439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098697
X-RAY DIFFRACTIONf_angle_d1.27211871
X-RAY DIFFRACTIONf_dihedral_angle_d16.1133135
X-RAY DIFFRACTIONf_chiral_restr0.0551268
X-RAY DIFFRACTIONf_plane_restr0.0071558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.77720.29641330.25553606X-RAY DIFFRACTION94
2.7772-2.85220.30341410.25483838X-RAY DIFFRACTION100
2.8522-2.93610.28941430.2373855X-RAY DIFFRACTION100
2.9361-3.03090.34821390.23123812X-RAY DIFFRACTION100
3.0309-3.13920.35031400.23913854X-RAY DIFFRACTION100
3.1392-3.26490.28831400.23813835X-RAY DIFFRACTION100
3.2649-3.41340.29411430.22863876X-RAY DIFFRACTION100
3.4134-3.59330.24021430.19233881X-RAY DIFFRACTION100
3.5933-3.81830.21261430.17193880X-RAY DIFFRACTION100
3.8183-4.1130.19951430.15633881X-RAY DIFFRACTION100
4.113-4.52660.16191440.13773932X-RAY DIFFRACTION100
4.5266-5.18080.17311450.13543937X-RAY DIFFRACTION100
5.1808-6.52440.19341450.15863976X-RAY DIFFRACTION100
6.5244-46.20910.18341540.16324133X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.3254 Å / Origin y: -8.4797 Å / Origin z: -11.2197 Å
111213212223313233
T0.3451 Å2-0.0363 Å2-0.0149 Å2-0.3402 Å2-0.0054 Å2--0.3902 Å2
L0.239 °2-0.0773 °2-0.4856 °2-0.1357 °2-0.1176 °2--1.2366 °2
S0.0125 Å °0.0187 Å °0.0451 Å °0.0134 Å °-0.0389 Å °-0.0357 Å °-0.1648 Å °0.0409 Å °0.0324 Å °
Refinement TLS groupSelection details: ALL

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