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- PDB-4bds: Human butyrylcholinesterase in complex with tacrine -

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Basic information

Entry
Database: PDB / ID: 4bds
TitleHuman butyrylcholinesterase in complex with tacrine
ComponentsCHOLINESTERASE
KeywordsHYDROLASE / NERVE TRANSMISSION / INHIBITIOR / ALPHA-BETA HYDROLASE
Function / homology
Function and homology information


cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / Neurotransmitter clearance / cholinesterase activity / choline binding / response to folic acid / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / acetylcholinesterase activity / choline metabolic process / hydrolase activity, acting on ester bonds / Aspirin ADME / nuclear envelope lumen / Synthesis of PC / Synthesis, secretion, and deacylation of Ghrelin / catalytic activity / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / negative regulation of cell population proliferation / endoplasmic reticulum lumen / 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
1-formyl-L-proline / alpha-L-fucopyranose / TACRINE / Cholinesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNachon, F. / Carletti, E. / Ronco, C. / Trovaslet, M. / Nicolet, Y. / Jean, L. / Renard, P.-Y.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal Structures of Human Cholinesterases in Complex with Huprine W and Tacrine: Elements of Specificity for Anti-Alzheimer'S Drugs Targeting Acetyl- and Butyrylcholinesterase.
Authors: Nachon, F. / Carletti, E. / Ronco, C. / Trovaslet, M. / Nicolet, Y. / Jean, L. / Renard, P.
History
DepositionOct 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Apr 9, 2014Group: Atomic model / Derived calculations / Non-polymer description
Revision 2.0Nov 15, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 4.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)62,60022
Polymers59,7141
Non-polymers2,88721
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.660, 155.660, 127.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-2129-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHOLINESTERASE / / BUTYRYLCHOLINESTERASE / ACYLCHOLINE ACYLHYDROLASE / BUTYRYLCHOLINE ESTERASE / CHOLINE ESTERASE II / ...BUTYRYLCHOLINESTERASE / ACYLCHOLINE ACYLHYDROLASE / BUTYRYLCHOLINE ESTERASE / CHOLINE ESTERASE II / PSEUDOCHOLINESTERASE


Mass: 59713.512 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 29-557 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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, 7 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.: 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
#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 / N-Acetylglucosamine


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
#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 293 molecules

#5: Chemical ChemComp-THA / TACRINE / Tacrine


Mass: 198.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2 / Comment: inhibitor, agonist*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-FPK / 1-formyl-L-proline


Type: L-peptide linking / Mass: 143.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO3
#10: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFPK IS BOUND TO THE OXYANION HOLE OF THE ENZYME, WHICH OFTEN LEADS TO THE DISTORTION OF SOME BONDS.

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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: 3.2 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5 / Details: 0.1 M MES PH 6.5, 2.1 M AMMONIUM SULFATE, 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→40.9 Å / Num. obs: 45776 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 34.86 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.4
Reflection shellResolution: 2.1→2.4 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P0I

1p0i


Resolution: 2.1→40.904 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 1422 3.1 %
Rwork0.1755 --
obs0.1765 45772 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 192 279 4646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094548
X-RAY DIFFRACTIONf_angle_d1.1356192
X-RAY DIFFRACTIONf_dihedral_angle_d19.7961694
X-RAY DIFFRACTIONf_chiral_restr0.08676
X-RAY DIFFRACTIONf_plane_restr0.005778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1750.29081470.24724332X-RAY DIFFRACTION100
2.175-2.26210.25961420.22924389X-RAY DIFFRACTION100
2.2621-2.36510.24481270.20594409X-RAY DIFFRACTION100
2.3651-2.48970.23911570.19324384X-RAY DIFFRACTION100
2.4897-2.64570.26831450.18944407X-RAY DIFFRACTION100
2.6457-2.84990.25441480.18064394X-RAY DIFFRACTION100
2.8499-3.13660.19841290.18124453X-RAY DIFFRACTION100
3.1366-3.59030.21461420.16614453X-RAY DIFFRACTION100
3.5903-4.52240.16551370.14444497X-RAY DIFFRACTION100
4.5224-40.91190.19041480.17164632X-RAY DIFFRACTION99
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)
12.6622-0.5986-0.21272.21350.22191.3772-0.13460.69860.2149-0.75330.12150.1332-0.2378-0.21380.04550.5993-0.1051-0.14460.4181-0.07540.282132.9016127.984917.3185
21.11050.6579-1.040.7403-1.17452.4035-0.19340.1231-0.3089-0.29170.0851-0.06610.4867-0.2820.07990.3708-0.0999-0.08630.2869-0.0810.4113130.2196111.472832.4519
31.8228-0.02590.63981.94330.04322.0755-0.0710.16740.041-0.33990.10760.036-0.2002-0.0484-0.02840.2468-0.0524-0.03680.1603-0.04350.205137.9794130.671930.9152
41.49930.15110.26081.95090.19162.21190.0169-0.16810.00840.02860.00820.1424-0.1279-0.2212-0.04260.1875-0.0008-0.06730.1969-0.05750.207136.1026131.209647.5354
51.77630.0893-0.96453.87151.58855.6974-0.22130.2033-0.6324-0.17480.2905-0.44120.92790.9187-0.09520.48930.08080.01230.4291-0.20270.6282152.3616107.559428.2685
65.25440.6091.4113.5359-0.64613.29920.2434-0.5473-0.4980.36790.062-0.21910.3991-0.1686-0.28840.3803-0.0432-0.1610.24870.02480.3708142.2188110.635658.2482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 1:65
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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