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- PDB-8qtw: Structure of human butyrylcholinesterase with (3-(((2-cycloheptyl... -

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Basic information

Entry
Database: PDB / ID: 8qtw
TitleStructure of human butyrylcholinesterase with (3-(((2-cycloheptylethyl)(methyl)amino)methyl)-1H-indol-7-yl)(methyl)carbamoylated Ser198
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / Inhibitor complex / Carbamate / Covalent
Function / homology
Function and homology information


cholinesterase / cocaine metabolic process / neuroblast differentiation / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / negative regulation of synaptic transmission / response to folic acid / acetylcholine catabolic process ...cholinesterase / cocaine metabolic process / neuroblast differentiation / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / negative regulation of synaptic transmission / response to folic acid / acetylcholine catabolic process / response to alkaloid / 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 / response to glucocorticoid / xenobiotic metabolic process / 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, 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
Similarity search - Domain/homology
GLYCOLIC ACID / N-acetyl-alpha-neuraminic acid / : / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsBrazzolotto, X. / Meden, A. / Knez, D. / Gobec, S. / Nachon, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-2316 France
CitationJournal: To Be Published
Title: Structure of human butyrylcholinesterase with (3-(((2-cycloheptylethyl)(methyl)amino)methyl)-1H-indol-7-yl)(methyl)carbamoylated Ser198
Authors: Brazzolotto, X. / Meden, A. / Knez, D. / Gobec, S. / Nachon, F.
History
DepositionOct 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: 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)64,31020
Polymers59,7141
Non-polymers4,59619
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint23 kcal/mol
Surface area21620 Å2
Unit cell
Length a, b, c (Å)154.231, 154.231, 127.979
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 enginered 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
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 5 types, 7 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#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: 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
#9: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 174 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#10: Chemical ChemComp-WXR / N-[3-[[2-cycloheptylethyl(methyl)amino]methyl]-1H-indol-7-yl]-N-methyl-methanamide


Mass: 341.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31N3O / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.19 Å3/Da / Density % sol: 61.4 %
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: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 2.24→55.19 Å / Num. obs: 36701 / % possible obs: 98.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 51.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05438 / Rpim(I) all: 0.02057 / Rrim(I) all: 0.05833 / Net I/σ(I): 19.79
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.6859 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 3644 / CC1/2: 0.887 / Rpim(I) all: 0.2606 / Rrim(I) all: 0.7359 / % possible all: 99.21

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→55.19 Å / SU ML: 0.2734 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1823 4.97 %
Rwork0.1778 34856 -
obs0.1799 36679 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.11 Å2
Refinement stepCycle: LAST / Resolution: 2.24→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 300 162 4657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00884656
X-RAY DIFFRACTIONf_angle_d0.95856327
X-RAY DIFFRACTIONf_chiral_restr0.0561710
X-RAY DIFFRACTIONf_plane_restr0.0089784
X-RAY DIFFRACTIONf_dihedral_angle_d9.8342711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.3391560.29132662X-RAY DIFFRACTION99.16
2.3-2.370.26351260.26622665X-RAY DIFFRACTION99.25
2.37-2.450.30731340.25052667X-RAY DIFFRACTION99.54
2.45-2.530.28991240.23742681X-RAY DIFFRACTION99.19
2.53-2.630.26331450.21892662X-RAY DIFFRACTION99.19
2.63-2.750.27291260.19282689X-RAY DIFFRACTION99.15
2.75-2.90.23241510.1892653X-RAY DIFFRACTION98.52
2.9-3.080.22111360.19122662X-RAY DIFFRACTION98.66
3.08-3.320.25031460.1832668X-RAY DIFFRACTION98.49
3.32-3.650.20771430.1662680X-RAY DIFFRACTION98.23
3.65-4.180.1861410.1512684X-RAY DIFFRACTION98.19
4.18-5.270.16971550.14282701X-RAY DIFFRACTION97.71
5.27-55.190.22691400.18072782X-RAY DIFFRACTION95.77
Refinement TLS params.Method: refined / Origin x: 31.9393150588 Å / Origin y: -16.7129625559 Å / Origin z: 38.9361868963 Å
111213212223313233
T0.37972195823 Å20.037450581266 Å20.0451898886918 Å2-0.418822204109 Å2-0.0432561049776 Å2--0.51708055421 Å2
L1.45261001948 °2-0.211896836206 °2-0.180231115385 °2-1.48350876417 °20.253079524625 °2--1.81981523789 °2
S0.0872733843144 Å °0.127260876474 Å °0.000808685750621 Å °-0.00524464266822 Å °-0.0311184438225 Å °-0.107359790524 Å °0.0409990903678 Å °0.116099871183 Å °-0.0596373850309 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 4 through 529 )

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