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- PDB-7bo4: Human Butyrylcholinesterase in complex with 3-(2-(butyl(2-cyclohe... -

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Basic information

Entry
Database: PDB / ID: 7bo4
TitleHuman Butyrylcholinesterase in complex with 3-(2-(butyl(2-cycloheptylethyl)amino)ethyl)-1H-indol-6-ol
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / Complex / Inhibitor
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 / Aspirin ADME / Synthesis of PC / nuclear envelope lumen / 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
Chem-A87 / METHANOL / N-acetyl-alpha-neuraminic acid / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsBrazzolotto, X. / Meden, A. / Knez, D. / Nachon, F. / Gobec, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-4210 France
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: From tryptophan-based amides to tertiary amines: Optimization of a butyrylcholinesterase inhibitor series.
Authors: Meden, A. / Knez, D. / Brazzolotto, X. / Nachon, F. / Dias, J. / Svete, J. / Stojan, J. / Groselj, U. / Gobec, S.
History
DepositionJan 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,65815
Polymers59,7141
Non-polymers3,94514
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint14 kcal/mol
Surface area21860 Å2
Unit cell
Length a, b, c (Å)155.300, 155.300, 128.060
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
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 4 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-ROHGlycam 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
[][D-1-deoxy-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.: 3
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
#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
#8: 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: isolated from a natural source / 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 , 5 types, 102 molecules

#5: 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
#6: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH4O
#7: Chemical ChemComp-A87 / 3-[2-[butyl(2-cycloheptylethyl)amino]ethyl]-1~{H}-indol-6-ol


Mass: 356.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C23H36N2O / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 61.41 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.401→49.4 Å / Num. obs: 30671 / % possible obs: 99.58 % / Redundancy: 26.9 % / Biso Wilson estimate: 57.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1548 / Rpim(I) all: 0.03031 / Rrim(I) all: 0.1578 / Net I/σ(I): 16.51
Reflection shellResolution: 2.401→2.487 Å / Rmerge(I) obs: 2.179 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 2922 / CC1/2: 0.637 / Rpim(I) all: 0.4271 / Rrim(I) all: 2.222

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PHENIX1.19_4092refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p0i

1p0i


Resolution: 2.401→49.4 Å / SU ML: 0.305 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 1534 5 %Random
Rwork0.1848 29128 --
obs0.1863 30662 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.25 Å2
Refinement stepCycle: LAST / Resolution: 2.401→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 257 95 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094651
X-RAY DIFFRACTIONf_angle_d0.94066327
X-RAY DIFFRACTIONf_chiral_restr0.0558709
X-RAY DIFFRACTIONf_plane_restr0.0078784
X-RAY DIFFRACTIONf_dihedral_angle_d12.4762699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.401-2.480.35421320.26872498X-RAY DIFFRACTION95.99
2.48-2.570.33021370.26832612X-RAY DIFFRACTION99.89
2.57-2.670.34621390.26092628X-RAY DIFFRACTION99.96
2.67-2.790.29931380.23472618X-RAY DIFFRACTION100
2.79-2.940.26331380.2182633X-RAY DIFFRACTION100
2.94-3.120.25241390.21322645X-RAY DIFFRACTION99.96
3.12-3.360.2211400.20162647X-RAY DIFFRACTION99.93
3.36-3.70.22231390.17342641X-RAY DIFFRACTION100
3.7-4.240.16681410.15342685X-RAY DIFFRACTION100
4.24-5.340.17881420.14692696X-RAY DIFFRACTION100
5.34-49.110.21591490.18382825X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61489220852-0.0327166802072-0.2278865189722.21907549152-0.0255919083241.68927314235-0.07530248866390.2665062691010.0234356718749-0.4997227062240.0856245162245-0.07044340718030.05465735244510.10065567319-0.04348418841410.541123342271-0.05732944349420.04552847870820.4430351736120.04318396315990.41389327949320.275807389528.923008733626.0899449919
21.50301103172-0.2967795497010.1232300150052.70492058465-1.57404842823.29073154666-0.1265852596410.1645624664360.489538113756-0.08474362301290.2349069577520.243290053723-0.527161557844-0.428097506904-0.1216221787760.4839943798870.0113883082177-0.02526879464310.5126299878960.07078238816770.5432160124174.3389759707338.350308203133.1931330085
34.30666154980.75669780539-1.290939619954.044626819191.055261499232.552331492240.227432813632-0.6275287606690.4028989143320.3490769080310.1087771807580.0390561530205-0.433014636470.173240287211-0.3302463914340.533704169539-0.03309797238260.08199874917790.497161920875-0.0121545465470.46261378910415.865426466344.867913536457.5899691623
42.022854728090.180659878621-0.8115813724463.635138077750.4692666964812.42826248654-0.019122015291-0.378228574508-0.04290245183770.2215159589750.0346042700936-0.08168296865190.0841586921110.256898290778-0.02261714697740.3776830790320.0133242999318-0.02658573461880.4170609414860.06531691178930.29937369105821.424247039924.927974172450.4615396161
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 209 )4 - 2091 - 206
22chain 'A' and (resid 210 through 316 )210 - 316207 - 313
33chain 'A' and (resid 317 through 397 )317 - 397314 - 394
44chain 'A' and (resid 398 through 529 )398 - 529395 - 526

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