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- PDB-6eqq: Human butyrylcholinesterase in complex with huprine 19 -

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Basic information

Entry
Database: PDB / ID: 6eqq
TitleHuman butyrylcholinesterase in complex with huprine 19
ComponentsCholinesterase
KeywordsHYDROLASE / Complex / Inhibitor / huprine
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
BROMIDE ION / huprine 19 / Unknown ligand / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40000447819 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 15, 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)62,81921
Polymers59,7141
Non-polymers3,10620
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-36 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.297, 154.297, 134.110
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 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.: 1
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
#3: Polysaccharide beta-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
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 7 types, 223 molecules

#4: Chemical ChemComp-H19 / huprine 19


Mass: 314.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21ClN3
#6: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES buffer, 2.1 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→57.13 Å / Num. obs: 31862 / % possible obs: 99.91 % / Redundancy: 9.5 % / Biso Wilson estimate: 46.4867618287 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09373 / Rpim(I) all: 0.03181 / Rrim(I) all: 0.0991 / Net I/σ(I): 17.14
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 3154 / CC1/2: 0.807 / Rpim(I) all: 0.3206 / Rrim(I) all: 0.9772 / % possible all: 100

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Processing

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

1p0i


Resolution: 2.40000447819→57.1280859052 Å / SU ML: 0.218521836804 / Cross valid method: FREE R-VALUE / σ(F): 1.34365534751 / Phase error: 21.4809239337
RfactorNum. reflection% reflectionSelection details
Rfree0.195683987417 1593 5.00062782521 %Random selection
Rwork0.1707807062 ---
obs0.172128929647 31856 99.9247176913 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.3772836568 Å2
Refinement stepCycle: LAST / Resolution: 2.40000447819→57.1280859052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 190 209 4594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003342683007984524
X-RAY DIFFRACTIONf_angle_d0.6292575231846158
X-RAY DIFFRACTIONf_chiral_restr0.0456791451711671
X-RAY DIFFRACTIONf_plane_restr0.00408965651156776
X-RAY DIFFRACTIONf_dihedral_angle_d9.754178989613604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.3135447923971430.2526011166442709X-RAY DIFFRACTION100
2.4775-2.5660.2680429525641420.2320600881222713X-RAY DIFFRACTION99.9649859944
2.566-2.66880.254123907251430.2184907705772715X-RAY DIFFRACTION99.9650227352
2.6688-2.79020.2493966278431440.204653905972720X-RAY DIFFRACTION100
2.7902-2.93730.1938619714521430.1819308228782719X-RAY DIFFRACTION99.9650716032
2.9373-3.12130.2177906450841440.17844260172737X-RAY DIFFRACTION99.9653018737
3.1213-3.36230.2071690937041430.1775501147492736X-RAY DIFFRACTION99.9652777778
3.3623-3.70060.1973884006661440.1551213486782731X-RAY DIFFRACTION99.9652294854
3.7006-4.2360.164818613411470.1378009891142768X-RAY DIFFRACTION99.8971898561
4.236-5.33620.1445667437151470.1394196255742808X-RAY DIFFRACTION100
5.3362-57.14420.2017125648271530.1856306130182907X-RAY DIFFRACTION99.512195122
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)
12.147364007611.030015817-0.136875929283.54770738858-0.5114217100231.456287178810.01550669831670.5629712348630.145211586158-0.705040495342-0.101106558110.0452888837773-0.1377586668850.05220628930730.0684286877170.5739196828350.0963028086164-0.007154915836650.6186288878930.1231404264930.382806439778-28.094406142422.1487133586-48.123859791
20.425629648142-0.625635092482-0.9076714524641.303253355171.206483362182.155829857160.1167689490410.204709082213-0.163183002404-0.117758460544-0.2009636226290.195682728184-0.296791273177-0.6097446407310.02652655033940.4643430000770.104659789982-0.02883449677960.514750147160.1107375226680.565834643051-44.345677367124.6305262931-33.007698186
31.97352225734-0.158980857540.000110650949492.03508563782-0.7166179448412.033643887730.1106750783550.3078971985710.137683131374-0.267385923538-0.003072261289960.0417511740327-0.02510689780620.166455832818-0.08901509528020.2647527520190.0339515530144-0.04965717043890.3195860997790.02205293854150.307236159363-25.260237476717.3220763219-34.651563854
42.21859788794-0.457712330264-0.2204381230211.895062422090.02581070684581.495092954850.0221903120505-0.1531390910220.2170038020270.2036020573230.0529934410147-0.0794539613544-0.1485516971820.0884490628364-0.1012361500820.3315704171650.0111091923213-0.07436560560030.3186277653430.05534302899290.365519421236-24.48223710619.1107495803-18.1752163352
53.791566654250.9427529376252.027098653073.936824758212.719467650995.609798975370.1050149815740.194268728189-0.216838980283-0.165486048924-0.2732242205510.7574248266580.659637866414-0.8072341856520.1408558236230.463442890386-0.0129554721142-0.1372093955870.603936063528-0.02344310901530.710040504644-47.95726333352.53264498905-36.9324930386
63.40165235773-1.43006560343-0.4292543345154.92217007054-0.7111269883923.22552382959-0.134614944674-0.361471728622-0.04328080144380.6424998665530.2648497686010.316294314209-0.00205721034475-0.301838880522-0.1385372192710.4342524218210.0298035954347-0.007957362349830.4577778935580.1187998237020.403638636882-44.304411893413.1134987309-6.47356028689
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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