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- PDB-8am2: Human butyrylcholinesterase in complex with 2,2'-(((1E,1'E)-(2-ph... -

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Basic information

Entry
Database: PDB / ID: 8am2
TitleHuman butyrylcholinesterase in complex with 2,2'-(((1E,1'E)-(2-phenylpyrimidine-4,6-diyl)bis(methaneylylidene))bis(hydrazin-1-yl-2-ylidene))bis(N,N,N-trimethyl-2-oxoethan-1-aminium)
ComponentsCholinesterase
KeywordsHYDROLASE / Inhibitor / complex / butyrylcholinesterase
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / hydrolase activity, acting on ester bonds / 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 ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N0C / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNachon, F. / Brazzolotto, X. / Dias, J.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-4210 France
CitationJournal: Chembiochem / Year: 2022
Title: Grid-Type Quaternary Metallosupramolecular Compounds Inhibit Human Cholinesterases through Dynamic Multivalent Interactions.
Authors: Nachon, F. / Brazzolotto, X. / Dias, J. / Courageux, C. / Drozdz, W. / Cao, X.Y. / Stefankiewicz, A.R. / Lehn, J.M.
History
DepositionAug 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 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)62,76516
Polymers59,7141
Non-polymers3,05115
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-37 kcal/mol
Surface area21510 Å2
Unit cell
Length a, b, c (Å)154.940, 154.940, 127.970
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
Source method: isolated from a genetically manipulated source
Details: engineered butyrylcholinesterase for crystallisation
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 2 types, 6 molecules

#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-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.: 4 / 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 , 5 types, 190 molecules

#3: Chemical ChemComp-N0C / ~{N}-[(~{E})-[2-phenyl-6-[[2-[2-(trimethyl-$l^{4}-azanyl)ethanoyl]hydrazinyl]methyl]pyrimidin-4-yl]methylideneamino]-2-(trimethyl-$l^{4}-azanyl)ethanamide


Mass: 442.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H34N8O2 / Feature type: SUBJECT OF INVESTIGATION
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: AMMONIUM SULFATE 2.1 M, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07252 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07252 Å / Relative weight: 1
ReflectionResolution: 2.5→55.25 Å / Num. obs: 26526 / % possible obs: 97.46 % / Redundancy: 6.4 % / Biso Wilson estimate: 46.82 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05889 / Rpim(I) all: 0.02449 / Rrim(I) all: 0.06401 / Net I/σ(I): 25.04
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4761 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 2653 / CC1/2: 0.89 / CC star: 0.971 / Rpim(I) all: 0.1955 / Rrim(I) all: 0.5164 / % possible all: 98.77

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0I

1p0i


Resolution: 2.5→55.25 Å / SU ML: 0.2806 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5561
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 1060 4 %
Rwork0.1702 25458 -
obs0.1721 26518 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 193 181 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834545
X-RAY DIFFRACTIONf_angle_d0.95726180
X-RAY DIFFRACTIONf_chiral_restr0.0589676
X-RAY DIFFRACTIONf_plane_restr0.0074783
X-RAY DIFFRACTIONf_dihedral_angle_d14.1916650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.30291320.23363163X-RAY DIFFRACTION98.53
2.61-2.750.29141320.21113178X-RAY DIFFRACTION98.69
2.75-2.920.24211310.20123155X-RAY DIFFRACTION98.15
2.92-3.150.2721320.20743169X-RAY DIFFRACTION98.13
3.15-3.470.2871330.17333170X-RAY DIFFRACTION97.72
3.47-3.970.19621320.15343172X-RAY DIFFRACTION97.29
3.97-50.16521320.12983184X-RAY DIFFRACTION96.7
5-55.250.21360.17553267X-RAY DIFFRACTION94.87
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)
13.52295161091-0.8717044059710.06435050098641.42606012965-0.01187345935021.833185480160.04171233885360.7824336398230.0941901401747-0.594964271992-0.05246607808640.169213104805-0.204038074905-0.1671119804810.01868820360430.652953764506-0.0731475401814-0.1415244413890.496133521268-0.008365044648450.379590272196132.057557779127.54935387817.5082513514
21.875195746841.18996502267-1.595743532081.44875071673-1.679941438452.82947647789-0.3005543419740.192489981238-0.176121890261-0.2917117301390.301466298955-0.2507785131720.640169075014-0.15180726455-0.05476388122060.525327962025-0.0888646153285-0.05320617154780.445192174908-0.06395176050960.427056906098129.595156586110.99134732232.4581375749
31.63976897415-0.2866262504070.3806376377582.022862231350.04885727729971.69763836127-0.000746601715320.157816144771-0.11044086148-0.3494562350960.04919826479670.142768910524-0.0322171731883-0.0957966410463-0.04460368667660.378939626592-0.0457307726214-0.03472397554130.303280318553-0.02671564920120.295914600234137.379662261130.07219712231.034587627
41.28722747456-0.073181121991-0.1332814997312.157123688550.03268711111392.384578763890.0194718596015-0.2258109663290.0405241071120.1306489254580.03730914764760.165372701938-0.0560597670458-0.199303981577-0.05478413359350.263949621785-0.0122508024106-0.04229430343350.289609627803-0.03355832028870.264561642921135.460986508130.62785759747.5844055913
53.1590164425-1.32417395689-2.139435560994.544645276242.567951469147.63457099676-0.2729267663040.134201553674-0.5639679290490.0196378602190.366448875154-0.5384576520.9777918808840.862943797813-0.1117900362610.5472024378410.04315361532830.04021291706110.481399037003-0.1313731176360.643301185954151.614331015107.18413495128.3339566188
67.630573741661.958311445031.975745004614.99249249654-0.8077524141383.73854633310.231869353264-0.747579148666-0.2120912421930.403956714839-0.0848755875707-0.1028688921210.182424486341-0.183995496732-0.1727754584740.4154690130520.00137636672952-0.05923598790860.3237544318010.01823933963240.302454533701141.42286948110.18845488558.7281082783
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 resseq 1:653 - 651 - 63
22chain A and resseq 66:9166 - 9164 - 89
33(chain A and resseq 92:153) or (chain A and resseq 164:231)92 - 23190 - 229
44(chain A and resseq 290:326) or (chain A and resseq 397:515)290 - 515288 - 513
55(chain A and resseq 154:163) or (chain A and resseq 232:289)154 - 289152 - 287
66(chain A and resseq 327:396) or (chain A and resseq 516:529)327 - 529325 - 527

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