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- PDB-6ntm: Crystal Structure of Recombinant Human Acetylcholinesterase Inhib... -

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Basic information

Entry
Database: PDB / ID: 6ntm
TitleCrystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-232 in Complex with the Reactivator, HI-6
ComponentsAcetylcholinesterase
Keywordshydrolase/hydrolase inhibitor / hydrolase / inhibitor / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / retina development in camera-type eye / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleus / membrane / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-HI6 / Chem-L0S / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsBester, S.M. / Guelta, M.A. / Height, J.J. / Pegan, S.D.
CitationJournal: To Be Published
Title: Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents
Authors: Height, J.J. / Bester, S.M. / Guelta, M.A. / Bae, S.Y. / Cheung, J. / Pegan, S.D.
History
DepositionJan 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)121,81610
Polymers118,8942
Non-polymers2,9228
Water5,801322
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,81610
Polymers118,8942
Non-polymers2,9228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,x,-z1
Buried area5860 Å2
ΔGint34 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.277, 105.277, 324.649
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59447.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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.: 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

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Non-polymers , 3 types, 326 molecules

#3: Chemical ChemComp-L0S / methyl (R)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidate / A-232


Mass: 206.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19N2O2P
#4: Chemical ChemComp-HI6 / 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM / 1-(2-HYDROXY-IMINOMETHYLPYRIDINIUM)-1-(4-CARBOXYAMINO)-PYRIDINIUM DIMETHYLETHER


Mass: 288.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15-21% polyethylene glycol 3350 (PEG) and 0.17- 0.21M potassium nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 68613 / % possible obs: 99.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Net I/σ(I): 15.2
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3245 / CC1/2: 0.921 / Rpim(I) all: 0.222 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.552→39.746 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.9
RfactorNum. reflection% reflection
Rfree0.2328 3371 4.94 %
Rwork0.1921 --
obs0.1941 68190 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.552→39.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8245 0 194 322 8761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038802
X-RAY DIFFRACTIONf_angle_d0.73412057
X-RAY DIFFRACTIONf_dihedral_angle_d3.1846971
X-RAY DIFFRACTIONf_chiral_restr0.0581300
X-RAY DIFFRACTIONf_plane_restr0.0051583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5523-2.58870.37321440.3222464X-RAY DIFFRACTION92
2.5887-2.62740.3561150.31522678X-RAY DIFFRACTION97
2.6274-2.66840.31211330.29392610X-RAY DIFFRACTION98
2.6684-2.71220.34831440.28322681X-RAY DIFFRACTION99
2.7122-2.75890.32521450.26762702X-RAY DIFFRACTION99
2.7589-2.80910.30561250.27042638X-RAY DIFFRACTION99
2.8091-2.86310.3721590.26472674X-RAY DIFFRACTION100
2.8631-2.92150.29431410.25822686X-RAY DIFFRACTION99
2.9215-2.9850.32681360.2382649X-RAY DIFFRACTION99
2.985-3.05440.25741420.22112663X-RAY DIFFRACTION99
3.0544-3.13080.22811430.21712682X-RAY DIFFRACTION99
3.1308-3.21540.26871240.21622714X-RAY DIFFRACTION100
3.2154-3.310.24741660.21432683X-RAY DIFFRACTION100
3.31-3.41670.23151090.20482726X-RAY DIFFRACTION99
3.4167-3.53880.27091220.20392721X-RAY DIFFRACTION100
3.5388-3.68040.23121710.18372688X-RAY DIFFRACTION100
3.6804-3.84770.20371340.16732704X-RAY DIFFRACTION100
3.8477-4.05040.22871330.16072779X-RAY DIFFRACTION99
4.0504-4.30390.16931660.15962662X-RAY DIFFRACTION99
4.3039-4.63580.16941330.14192759X-RAY DIFFRACTION99
4.6358-5.10140.17741490.14242745X-RAY DIFFRACTION99
5.1014-5.83760.1851350.17392800X-RAY DIFFRACTION100
5.8376-7.34720.24461410.19132805X-RAY DIFFRACTION99
7.3472-39.75080.23561610.18532906X-RAY DIFFRACTION98
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)
12.53830.5248-0.71931.4764-0.06133.447-0.0458-0.29840.03560.12350.0127-0.00260.28660.23710.04580.52190.06280.00420.5594-0.02290.280251.2803-31.72134.2254
21.45970.1483-1.29371.1849-0.79072.907-0.01280.25770.0633-0.20560.06210.07590.247-0.2701-0.0630.5879-0.0306-0.02460.6401-0.00560.284746.9312-28.41810.9588
32.2388-1.08390.25131.84290.0472.56640.1268-0.04510.06810.0743-0.09970.0976-0.0919-0.3106-0.01610.4995-0.1220.01270.5605-0.0260.3418-4.9462-31.771936.8715
41.64770.34430.69291.32460.32284.11480.05090.0277-0.17980.0004-0.10660.03270.5203-0.22130.04680.5747-0.03040.0220.5622-0.04210.3366-0.4289-51.233423.0059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:334)
2X-RAY DIFFRACTION2(chain A and resid 335:542)
3X-RAY DIFFRACTION3(chain B and resid 5:321)
4X-RAY DIFFRACTION4(chain B and resid 322:542)

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