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- PDB-7d9o: Crystal Structure of Recombinant Human Acetylcholinesterase in Co... -

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Basic information

Entry
Database: PDB / ID: 7d9o
TitleCrystal Structure of Recombinant Human Acetylcholinesterase in Complex with Compound 2
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 / cell adhesion / hydrolase activity / 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-H0L / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 16, 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
Water4,360242
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 operation4_555y,x,-z1
Buried area3640 Å2
ΔGint12 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.866, 104.866, 324.416
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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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-H0L / (2R)-2-[[4-fluoranyl-1-[(4-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.: 242 / 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: 4.42 Å3/Da / Density % sol: 72.18 %
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: BL17U / 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: 2.45→50 Å / Num. obs: 76763 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 39.91 Å2 / Rmerge(I) obs: 0.296 / Rpim(I) all: 0.07 / Rrim(I) all: 0.305 / Χ2: 1.094 / Net I/σ(I): 3.9 / Num. measured all: 1450100
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.4914.72.8137630.7250.7382.9070.42399.9
2.49-2.5415.52.51337550.7550.6452.5970.433100
2.54-2.5918.82.24137770.8470.5282.3020.42100
2.59-2.6419.72.15537920.8410.4962.2120.427100
2.64-2.720.11.73638000.8850.3961.7810.561100
2.7-2.7620.41.56137870.9080.3521.60.429100
2.76-2.8320.21.30738210.9270.2971.340.444100
2.83-2.9200.99937690.9610.2281.0250.448100
2.9-2.9919.80.7938070.9690.1810.8110.469100
2.99-3.0919.50.58738050.980.1360.6030.502100
3.09-3.219.40.45738050.9840.1060.470.5399.9
3.2-3.32190.36137970.9840.0850.3710.61100
3.32-3.4818.40.28438440.990.0680.2920.84499.9
3.48-3.6616.10.21338150.9910.0540.221.067100
3.66-3.8919.40.1938680.9950.0440.1951.335100
3.89-4.1920.50.14138710.9960.0320.1451.585100
4.19-4.6120.20.11738440.9960.0270.122.20399.9
4.61-5.2819.70.10439010.9970.0240.1062.224100
5.28-6.6518.50.10139680.9960.0240.1042.428100
6.65-5017.90.06841740.9970.0160.074.087100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ey7

4ey7


Resolution: 2.45→49.89 Å / SU ML: 0.2804 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 3839 5.01 %
Rwork0.1871 72824 -
obs0.1884 76663 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.55 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8184 0 136 242 8562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00928645
X-RAY DIFFRACTIONf_angle_d1.231111842
X-RAY DIFFRACTIONf_chiral_restr0.07551283
X-RAY DIFFRACTIONf_plane_restr0.00731553
X-RAY DIFFRACTIONf_dihedral_angle_d18.3333120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.32441180.2822602X-RAY DIFFRACTION98.59
2.49-2.520.28591310.2692658X-RAY DIFFRACTION100
2.52-2.550.27771440.25192700X-RAY DIFFRACTION99.96
2.55-2.590.31291290.24472630X-RAY DIFFRACTION99.96
2.59-2.630.22641790.24062629X-RAY DIFFRACTION100
2.63-2.670.23281710.23342652X-RAY DIFFRACTION99.93
2.67-2.710.2414960.23232675X-RAY DIFFRACTION99.96
2.71-2.760.29561530.23172697X-RAY DIFFRACTION99.96
2.76-2.810.27561410.22282615X-RAY DIFFRACTION100
2.81-2.860.27561420.22442705X-RAY DIFFRACTION99.96
2.86-2.920.22871360.22552677X-RAY DIFFRACTION99.89
2.92-2.990.23241410.21692661X-RAY DIFFRACTION100
2.99-3.050.22921480.22882656X-RAY DIFFRACTION99.96
3.05-3.130.23231510.22412664X-RAY DIFFRACTION99.93
3.13-3.220.26941370.21692689X-RAY DIFFRACTION99.96
3.22-3.310.2261310.21332712X-RAY DIFFRACTION100
3.31-3.420.22271230.19812702X-RAY DIFFRACTION99.93
3.42-3.540.2561590.1952660X-RAY DIFFRACTION99.96
3.54-3.680.21821290.1822725X-RAY DIFFRACTION100
3.68-3.850.17421490.17232700X-RAY DIFFRACTION99.96
3.85-4.050.20041510.15062696X-RAY DIFFRACTION100
4.05-4.30.15941320.14852718X-RAY DIFFRACTION99.96
4.3-4.640.16561560.1362743X-RAY DIFFRACTION99.97
4.64-5.10.16711430.14422735X-RAY DIFFRACTION100
5.1-5.840.18991640.16052759X-RAY DIFFRACTION100
5.84-7.350.20551570.17462771X-RAY DIFFRACTION99.97
7.36-49.890.1861280.16542993X-RAY DIFFRACTION99.9

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