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- PDB-9r9e: Recombinant human butyrylcholinesterase in complex with N-(3-meth... -

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Basic information

Entry
Database: PDB / ID: 9r9e
TitleRecombinant human butyrylcholinesterase in complex with N-(3-methoxypropyl)-N-{[1-(prop-2-yn-1-yl)pyrrolidin-3-yl]methyl}naphthalene-2-sulfonamide
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / inhibitor / complex
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / response to alkaloid / choline metabolic process / acetylcholine catabolic process / negative regulation of synaptic transmission / hydrolase activity, acting on ester bonds / peptide hormone processing / acetylcholinesterase activity / nuclear envelope lumen / Synthesis of PC / Aspirin ADME / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / identical protein binding / 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
: / ACETATE ION / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBrazzolotto, X. / Kosak, U. / Nachon, F. / Gobec, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-2316 France
CitationJournal: Chem.Biol.Interact. / Year: 2025
Title: N-Propargylpyrrolidine-based butyrylcholinesterase and monoamine oxidase inhibitors.
Authors: Kosak, U. / Knez, D. / Pislar, A. / Horvat, S. / Zakelj, S. / Igert, A. / Dias, J. / Nachon, F. / Brazzolotto, X. / Gobec, S.
History
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,24516
Polymers59,7141
Non-polymers3,53215
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-16 kcal/mol
Surface area21390 Å2
Unit cell
Length a, b, c (Å)154.403, 154.403, 127.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cholinesterase / Acylcholine acylhydrolase / Butyrylcholine esterase / Choline esterase II / Pseudocholinesterase


Mass: 59713.512 Da / Num. of mol.: 1
Mutation: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide)
Source method: isolated from a genetically manipulated source
Details: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide)
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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-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
#4: 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: obtained synthetically / 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 , 6 types, 181 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-A1JDO / ~{N}-(3-methoxypropyl)-~{N}-[[(3~{S})-1-prop-2-ynylpyrrolidin-3-yl]methyl]naphthalene-2-sulfonamide


Mass: 400.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N2O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.18→47.72 Å / Num. obs: 39152 / % possible obs: 96.38 % / Redundancy: 7.2 % / Biso Wilson estimate: 38.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1366 / Rpim(I) all: 0.05414 / Rrim(I) all: 0.1476 / Net I/σ(I): 10.93
Reflection shellResolution: 2.18→2.23 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.88 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2740 / CC1/2: 0.405 / Rpim(I) all: 0.7518 / Rrim(I) all: 2.034 / % possible all: 94.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→47.72 Å / SU ML: 0.2636 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 1957 5.05 %
Rwork0.1852 36825 -
obs0.187 38782 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.55 Å2
Refinement stepCycle: LAST / Resolution: 2.18→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 226 172 4593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724584
X-RAY DIFFRACTIONf_angle_d0.89786236
X-RAY DIFFRACTIONf_chiral_restr0.0545694
X-RAY DIFFRACTIONf_plane_restr0.0062780
X-RAY DIFFRACTIONf_dihedral_angle_d15.60971854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.31871500.28552482X-RAY DIFFRACTION94.07
2.23-2.290.2831520.26012613X-RAY DIFFRACTION96.95
2.29-2.360.27041630.24572569X-RAY DIFFRACTION96.57
2.36-2.440.32251530.24112614X-RAY DIFFRACTION97.22
2.44-2.530.27891420.23822649X-RAY DIFFRACTION97.83
2.53-2.630.28941320.22552650X-RAY DIFFRACTION97.72
2.63-2.750.28011260.22542640X-RAY DIFFRACTION97.19
2.75-2.890.231240.20582651X-RAY DIFFRACTION97.51
2.89-3.070.23771390.18952637X-RAY DIFFRACTION97.03
3.07-3.310.22311230.1842645X-RAY DIFFRACTION96.55
3.31-3.640.20921400.16782643X-RAY DIFFRACTION96.13
3.64-4.170.18811270.14582647X-RAY DIFFRACTION95.85
4.17-5.250.18551340.14152662X-RAY DIFFRACTION95.17
5.25-47.720.18121520.18512723X-RAY DIFFRACTION93.83
Refinement TLS params.Method: refined / Origin x: 16.686087633 Å / Origin y: 31.9333844545 Å / Origin z: 38.7968433962 Å
111213212223313233
T0.283490608474 Å2-0.0285193921333 Å20.0224811084339 Å2-0.279989668583 Å20.0526836278028 Å2--0.314889198152 Å2
L1.0705061616 °20.192995530453 °2-0.280591569805 °2-1.43744785579 °20.001142353094 °2--1.61882019965 °2
S-0.00665002454748 Å °0.0299547678289 Å °0.115436898402 Å °-0.153834550007 Å °0.0627918640046 Å °0.0152700290929 Å °-0.0870632139716 Å °0.0542090897826 Å °-0.0547897131256 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 4 through 529 )

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