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- PDB-6eqp: Human butyrylcholinesterase in complex with ethopropazine -

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Basic information

Entry
Database: PDB / ID: 6eqp
TitleHuman butyrylcholinesterase in complex with ethopropazine
ComponentsCholinesterase
KeywordsHYDROLASE / Complex / Inhibitor / Phenothiazine
Function / homology
Function and homology information


cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / response to alkaloid / choline binding / response to folic acid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / choline metabolic process / response to alkaloid / choline binding / response to folic acid / acetylcholine catabolic process / negative regulation of synaptic transmission / cholinesterase activity / peptide hormone processing / acetylcholinesterase activity / hydrolase activity, acting on ester bonds / nuclear envelope lumen / Aspirin ADME / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / 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, catalytic domain ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
R-ethopropazine / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34941708483 Å
AuthorsNachon, F. / Brazzolotto, X. / Wandhammer, M. / Trovaslet-Leroy, M. / Rosenberry, T.L. / Macdonald, I.R. / Darvesh, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Defense France
CitationJournal: Molecules / Year: 2017
Title: Comparison of the Binding of Reversible Inhibitors to Human Butyrylcholinesterase and Acetylcholinesterase: A Crystallographic, Kinetic and Calorimetric Study.
Authors: Rosenberry, T.L. / Brazzolotto, X. / Macdonald, I.R. / Wandhammer, M. / Trovaslet-Leroy, M. / Darvesh, S. / Nachon, F.
History
DepositionOct 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)62,60817
Polymers59,7141
Non-polymers2,89416
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-62 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.230, 155.230, 135.300
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
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Plasmid: pGS / Cell line (production host): CHO-K1 / 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.: 1
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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-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[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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, 247 molecules

#4: Chemical ChemComp-BUW / R-ethopropazine


Mass: 312.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 MES BUFFER, 2.1 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.349→54.89 Å / Num. obs: 34489 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 45.0985468454 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07518 / Rpim(I) all: 0.03156 / Rrim(I) all: 0.08175 / Net I/σ(I): 19.16
Reflection shellResolution: 2.349→2.433 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.8835 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 3379 / CC1/2: 0.805 / Rpim(I) all: 0.3698 / Rrim(I) all: 0.96 / % possible all: 98.57

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P0I

1p0i


Resolution: 2.34941708483→54.8820928218 Å / SU ML: 0.289756730965 / Cross valid method: FREE R-VALUE / σ(F): 1.34750961296 / Phase error: 27.0337061533
RfactorNum. reflection% reflectionSelection details
Rfree0.237233561589 1035 3.00243676027 %Random selection
Rwork0.187639981938 ---
obs0.189105463189 34472 99.5178844655 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.5565776099 Å2
Refinement stepCycle: LAST / Resolution: 2.34941708483→54.8820928218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 177 237 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003260070471884541
X-RAY DIFFRACTIONf_angle_d0.7017415790096194
X-RAY DIFFRACTIONf_chiral_restr0.0562571715876682
X-RAY DIFFRACTIONf_plane_restr0.00394504331798783
X-RAY DIFFRACTIONf_dihedral_angle_d10.45535021913616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3494-2.47330.3559080075411450.2864770532764684X-RAY DIFFRACTION98.9549180328
2.4733-2.62820.297333037991460.2591479630954728X-RAY DIFFRACTION99.8975199836
2.6282-2.83120.3006742057111460.2428778170974714X-RAY DIFFRACTION99.8766954377
2.8312-3.1160.275135282551480.2267899409344775X-RAY DIFFRACTION99.9390986602
3.116-3.56690.2522228102081480.199055196354777X-RAY DIFFRACTION99.9188476364
3.5669-4.49360.2045028886151480.1513802068414811X-RAY DIFFRACTION99.6583601286
4.4936-54.8970.2012603507611540.1575022360014948X-RAY DIFFRACTION98.4371985337
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)
11.689197511670.355057435478-0.0851155858152.312951101480.7596739162771.981817572230.02934781485590.579137739811-0.223394280039-0.732324949123-0.167063420207-0.01168670031050.0525011262569-0.1601494463270.1204032319560.5333745412030.09726773968920.05554888796750.618215819099-0.1448134302410.37515056401428.3601773492-22.212371599619.3350615967
20.916747370249-0.558289270940.6346419520891.05466190996-0.5715606489891.762377585730.1113494019020.3316926816290.0860111628006-0.0599304623021-0.197461894082-0.291134427689-0.04313251791930.5680385039940.03097501253910.4139385334650.0773623743780.08099968214850.500790643513-0.07887227528450.5257612249844.7686984583-24.616592861134.3841260751
32.33371836180.121267422616-0.04573350329591.940946417610.9939937782242.182491679160.1201459217310.354018228887-0.10492636317-0.259072200644-0.1047373727140.03813211258140.0373791122852-0.177804162666-0.003573356684220.2919467260110.05384475403350.04318983178960.362987449352-0.03367710623510.31739970658525.4791175244-17.211927012332.830644992
42.27683770925-0.191065321431-0.2748715005821.636074732740.2746310585361.544275090940.0359388461401-0.0935422975404-0.1765896412940.173306226050.01676958406770.0956672426370.168805570289-0.075313139407-0.07911207492030.3420676515410.01270444202260.05616897800650.325892548058-0.05104805012720.34730657695724.9239341059-19.30232733149.3406796648
52.528790810230.132493385923-1.079747021041.9992725891-0.6923985861643.673845827340.212994310740.1978519889210.342232838088-0.231167878283-0.370788823498-0.783478813105-1.016830508560.9380145177640.06820415286950.587259386524-0.04435272448270.2254623862170.6123851489390.04906075839010.74536873612548.2714952042-2.4848137780130.362158577
62.44719872435-0.5810729494180.562576147653.551120414371.285629514963.05782017248-0.0314219159746-0.2469431806690.04921492331230.4086585713390.302659731319-0.3100256472440.02665118597250.452004992949-0.2543595215540.4227740085940.0558480482509-0.00287039406710.49976746505-0.1254836981350.38870794495144.8865339563-13.06327702361.0709533453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 4:65
2X-RAY DIFFRACTION2chain A and resseq 66:91
3X-RAY DIFFRACTION3(chain A and resseq 92:153) or (chain A and resseq 164:231)
4X-RAY DIFFRACTION4(chain A and resseq 290:326) or (chain A and resseq 397:515)
5X-RAY DIFFRACTION5(chain A and resseq 154:163) or (chain A and resseq 232:289)
6X-RAY DIFFRACTION6(chain A and resseq 327:396) or (chain A and resseq 516:529)

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