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- PDB-8qtx: Structure of human butyrylcholinesterase with 3-(((2-cycloheptyle... -

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Basic information

Entry
Database: PDB / ID: 8qtx
TitleStructure of human butyrylcholinesterase with 3-(((2-cycloheptylethyl)(methyl)amino)methyl)-N-methyl-1H-indol-7-amine
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / Inhibitor / complex
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
CARBONATE ION / : / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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)-N-methyl-1H-indol-7-amine
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)63,50718
Polymers59,7141
Non-polymers3,79417
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-9 kcal/mol
Surface area21270 Å2
Unit cell
Length a, b, c (Å)154.639, 154.639, 127.643
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 , 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
#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

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Non-polymers , 6 types, 183 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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
#7: Chemical ChemComp-WXN / 3-(((2-cycloheptylethyl)(methyl)amino)methyl)-N-methyl-1H-indol-7-amine / 3-[[2-cycloheptylethyl(methyl)amino]methyl]-N-methyl-1H-indol-7-amine


Mass: 313.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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: 3.19 Å3/Da / Density % sol: 61.5 %
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: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.12→49.22 Å / Num. obs: 43198 / % possible obs: 98.05 % / Redundancy: 8.2 % / Biso Wilson estimate: 48.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08076 / Rpim(I) all: 0.02907 / Rrim(I) all: 0.08616 / Net I/σ(I): 13.31
Reflection shellResolution: 2.12→2.196 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 4130 / CC1/2: 0.42 / Rpim(I) all: 0.5604 / Rrim(I) all: 1.589 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→49.22 Å / SU ML: 0.2686 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 2091 4.85 %
Rwork0.1781 41009 -
obs0.1799 43100 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.66 Å2
Refinement stepCycle: LAST / Resolution: 2.12→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 243 172 4618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00854612
X-RAY DIFFRACTIONf_angle_d0.87556273
X-RAY DIFFRACTIONf_chiral_restr0.0549696
X-RAY DIFFRACTIONf_plane_restr0.0067783
X-RAY DIFFRACTIONf_dihedral_angle_d8.8084691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.37011260.32252592X-RAY DIFFRACTION94.31
2.17-2.220.35321420.2922705X-RAY DIFFRACTION98.61
2.22-2.280.29921270.24622730X-RAY DIFFRACTION98.72
2.28-2.350.29391410.23642738X-RAY DIFFRACTION99.55
2.35-2.430.25581340.22432740X-RAY DIFFRACTION99.24
2.43-2.510.27721400.21342727X-RAY DIFFRACTION99.17
2.51-2.610.25781460.21172727X-RAY DIFFRACTION99.07
2.61-2.730.21651270.20172753X-RAY DIFFRACTION99.04
2.73-2.880.22221450.18582761X-RAY DIFFRACTION98.94
2.88-3.060.20571510.1872706X-RAY DIFFRACTION98.48
3.06-3.290.23411330.18342739X-RAY DIFFRACTION97.85
3.29-3.620.21121400.16812741X-RAY DIFFRACTION97.89
3.63-4.150.1721440.14572755X-RAY DIFFRACTION97.94
4.15-5.230.18221430.13762767X-RAY DIFFRACTION97.39
5.23-49.220.21771520.18032828X-RAY DIFFRACTION95.06
Refinement TLS params.Method: refined / Origin x: 16.6971650636 Å / Origin y: 32.0424859467 Å / Origin z: 38.8970927023 Å
111213212223313233
T0.325010311327 Å2-0.0268877854062 Å20.0290322645643 Å2-0.307519177359 Å20.0415656158329 Å2--0.354983296826 Å2
L1.274030567 °20.240527359768 °2-0.299640331923 °2-1.44664470978 °2-0.198545936753 °2--1.84354205237 °2
S-0.000774857517722 Å °0.0200800227137 Å °0.118107007118 Å °-0.143863527283 Å °0.0548004818838 Å °0.00378976488518 Å °-0.0707631764058 Å °0.0427748726495 Å °-0.0571742807861 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 4 through 529 )

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