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- PDB-8am1: Human butyrylcholinesterase in complex with zinc and N,N,N-trimet... -

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Basic information

Entry
Database: PDB / ID: 8am1
TitleHuman butyrylcholinesterase in complex with zinc and N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium
ComponentsCholinesterase
KeywordsHYDROLASE / Inhibitor / complex / zinc / butyrylcholinesterase
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 / 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-LWL / AMMONIUM ION / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 1.2Nov 20, 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)63,14025
Polymers59,7141
Non-polymers3,42624
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-95 kcal/mol
Surface area21700 Å2
Unit cell
Length a, b, c (Å)154.910, 154.910, 134.970
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
#3: 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 , 7 types, 113 molecules

#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-LWL / N,N,N-trimethyl-2-oxo-2-(2-(pyridin-2-ylmethylene)hydrazineyl)ethan-1-aminium / ~{N}-[(~{E})-pyridin-2-ylmethylideneamino]-2-(trimethyl-$l^{4}-azanyl)ethanamide


Mass: 221.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N4O / Feature type: SUBJECT OF INVESTIGATION
#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: 3.39 Å3/Da / Density % sol: 63.72 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.53→109.54 Å / Num. obs: 27493 / % possible obs: 99.86 % / Redundancy: 10.6 % / Biso Wilson estimate: 57.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09455 / Rpim(I) all: 0.03056 / Rrim(I) all: 0.09948 / Net I/σ(I): 19.94
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.107 / Num. unique obs: 4575 / CC1/2: 0.831 / CC star: 0.953 / Rpim(I) all: 0.3482 / % possible all: 99.93

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0I

1p0i


Resolution: 2.53→109.54 Å / SU ML: 0.3627 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 1351 4.92 %
Rwork0.188 26125 -
obs0.1898 27476 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.6 Å2
Refinement stepCycle: LAST / Resolution: 2.53→109.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 208 95 4506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924561
X-RAY DIFFRACTIONf_angle_d0.97546192
X-RAY DIFFRACTIONf_chiral_restr0.0588676
X-RAY DIFFRACTIONf_plane_restr0.008786
X-RAY DIFFRACTIONf_dihedral_angle_d10.5795658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.630.37681230.32342588X-RAY DIFFRACTION99.93
2.63-2.730.33231480.28852554X-RAY DIFFRACTION100
2.73-2.850.31121440.2482569X-RAY DIFFRACTION100
2.86-3.010.28621440.2342556X-RAY DIFFRACTION99.85
3.01-3.190.30651310.24942588X-RAY DIFFRACTION99.96
3.19-3.440.27411340.19592601X-RAY DIFFRACTION99.85
3.44-3.790.2231330.17142619X-RAY DIFFRACTION99.89
3.79-4.330.17951240.15342620X-RAY DIFFRACTION99.96
4.33-5.460.17621500.14792630X-RAY DIFFRACTION99.53
5.46-109.540.19121200.182800X-RAY DIFFRACTION99.66
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)
14.94236542458-1.469342853560.1755842052561.65726845465-0.5041434617031.43351251582-0.06334355520030.865971330165-0.331761047828-0.4376720364320.0618338194870.2915174285560.09629294997-0.0783053666544-0.0238202748470.733252840279-0.152266531807-0.1373023281370.669790266512-0.06131010806490.603593499218-22.3401554597-28.129086665-48.3182242857
21.736554001610.726586667438-1.659264598321.03237060777-1.457676759743.63650544869-0.2458497693850.250508817377-0.456413853246-0.2768734191310.341313369815-0.3153319997750.972686026017-0.484140054615-0.1518625726420.668352997716-0.177045227704-0.13479971890.619843928313-0.06528148609170.822471353595-24.636983848-44.6207929779-33.1167704618
31.87750973938-0.5086062408710.7199818863811.566765560090.1314466477821.86916977583-0.02704220815860.229805714587-0.0880931523198-0.266824365310.07930517758520.120469206987-0.04043702293460.00969373814662-0.02675393302920.467061401575-0.0736372281644-0.03896853568470.369323801856-0.05537316599010.633535936458-17.0780769195-25.3885956308-34.7770176341
42.59397905661-0.526614843615-0.05194458800622.44357634606-0.1144173437912.08485930186-0.0285724764492-0.189482029636-0.01396396925790.05699796281580.1490581938550.134203282613-0.0129477716858-0.295141410243-0.1444369676050.396637878513-0.0451914817289-0.06435363493230.401244827884-0.03436837135990.565975794385-19.0001632599-24.7480797721-18.3117840406
55.88512490357-1.18912577737-4.154085460546.080966891182.386848726868.37686775735-0.3632812650560.29304080709-0.906721286024-0.2950192483780.334687784267-0.04982509765741.199619245230.6872380669170.06708224138810.688269572564-0.00622824263863-0.01162490655910.542627059066-0.1766861759820.880797848991-2.39197628158-48.1273198496-37.1512503928
68.424263235850.8484692158552.282420930854.43273942151-0.2233153514916.429316396170.229968849549-0.634919127299-0.3155400658670.344455092912-0.001435422764540.01166804962780.5865845989180.0316178474727-0.2204459038660.542309969187-0.00109655801039-0.07835119709570.4747873847590.002047929941330.666635261861-13.0376201711-44.7369402865-6.45797763309
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 3:653 - 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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