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- PDB-7d9q: Crystal Structure of Recombinant Human Acetylcholinesterase in Co... -

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Basic information

Entry
Database: PDB / ID: 7d9q
TitleCrystal Structure of Recombinant Human Acetylcholinesterase in Complex with Compound 7
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / AchE inhibitor / complex structure
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-H1R / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å
AuthorsLiu, Q.F. / Yin, W.C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Kinetics-Driven Drug Design Strategy for Next-Generation Acetylcholinesterase Inhibitors to Clinical Candidate.
Authors: Zhou, Y. / Fu, Y. / Yin, W. / Li, J. / Wang, W. / Bai, F. / Xu, S. / Gong, Q. / Peng, T. / Hong, Y. / Zhang, D. / Zhang, D. / Liu, Q. / Xu, Y. / Xu, H.E. / Zhang, H. / Jiang, H. / Liu, H.
History
DepositionOct 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)123,6236
Polymers121,6512
Non-polymers1,9724
Water88349
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6236
Polymers121,6512
Non-polymers1,9724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3650 Å2
ΔGint13 kcal/mol
Surface area36530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.649, 104.649, 324.403
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60825.508 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
#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-H1R / (2S)-2-[[4-fluoranyl-1-[(3-fluorophenyl)methyl]piperidin-4-yl]methyl]-5,6-dimethoxy-2,3-dihydroinden-1-one


Mass: 415.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27F2NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.22 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.16-0.22M potassium nitrate, 16-20% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 60606 / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.697 / Rpim(I) all: 0.168 / Rrim(I) all: 0.718 / Χ2: 1 / Net I/σ(I): 3.4 / Num. measured all: 1094103
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.712.66.78330080.5081.9447.0630.98199.9
2.7-2.7413.85.89229970.5461.66.1090.95699.9
2.74-2.815.15.60729310.6261.4585.7970.97399.9
2.8-2.8516.14.42430000.6721.1144.5650.968100
2.85-2.9217.43.99430020.8050.9734.1130.969100
2.92-2.9818.43.41329790.820.813.5090.996100
2.98-3.0619.12.74329920.8720.642.8170.974100
3.06-3.1419.42.23829850.9170.5182.2980.978100
3.14-3.2319.41.88329970.9120.4351.9340.985100
3.23-3.3419.21.33329850.9490.311.3690.998100
3.34-3.4618.91.0130170.9640.2371.0380.985100
3.46-3.616.80.66530240.9730.1660.6861.00399.9
3.6-3.76180.51129990.9790.1230.5261.004100
3.76-3.9620.60.38130250.9910.0850.3911.003100
3.96-4.2120.80.28430370.9930.0630.2911.016100
4.21-4.5320.40.19830580.9920.0450.2031.034100
4.53-4.9920.20.15330500.9940.0350.1571.037100
4.99-5.7119.40.15430790.9920.0350.1581.02100
5.71-7.19170.12131170.9930.030.1251.02299.9
7.19-5018.10.05533240.9960.0130.0561.061100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.57 Å49.8 Å
Translation4.57 Å49.8 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASER2.8.3phasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ey7

4ey7


Resolution: 2.66→49.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 2738 4.92 %
Rwork0.1832 52969 -
obs0.185 55707 92.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.33 Å2 / Biso mean: 42.6802 Å2 / Biso min: 19.18 Å2
Refinement stepCycle: final / Resolution: 2.66→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8187 0 136 49 8372
Biso mean--49.44 38.35 -
Num. residues----1056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.66-2.70.3294590.27581246130544
2.7-2.750.3083750.26481498157352
2.75-2.810.3108850.27311819190465
2.81-2.860.3407860.27072421250784
2.86-2.920.30841300.27472768289896
2.92-2.990.33731420.25422806294899
2.99-3.070.28091440.263628432987100
3.07-3.150.33461640.244628072971100
3.15-3.240.29521490.231128342983100
3.24-3.350.24851780.212128162994100
3.35-3.470.30211510.198828633014100
3.47-3.610.21571570.191928643021100
3.61-3.770.19851500.177128492999100
3.77-3.970.20221840.156128223006100
3.97-4.220.16161290.144729013030100
4.22-4.540.1661650.130828963061100
4.54-50.14741530.134828813034100
5-5.720.17751400.153329343074100
5.72-7.210.22121520.169229573109100
7.21-49.80.17411450.167331443289100

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