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- PDB-6xyy: Update of ACHE FROM DROSOPHILA MELANOGASTER COMPLEX WITH TACRINE ... -

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Entry
Database: PDB / ID: 6xyy
TitleUpdate of ACHE FROM DROSOPHILA MELANOGASTER COMPLEX WITH TACRINE DERIVATIVE 9-(3-PHENYLMETHYLAMINO)-1,2,3,4-TETRAHYDROACRIDINE
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / insect / inhibitor / complex
Function / homology
Function and homology information


Aspirin ADME / Neurotransmitter clearance / Synthesis of PC / choline catabolic process / sulfate binding / serine hydrolase activity / choline metabolic process / acetylcholine catabolic process in synaptic cleft / acetylcholine catabolic process / acetylcholinesterase ...Aspirin ADME / Neurotransmitter clearance / Synthesis of PC / choline catabolic process / sulfate binding / serine hydrolase activity / choline metabolic process / acetylcholine catabolic process in synaptic cleft / acetylcholine catabolic process / acetylcholinesterase / cholinesterase activity / acetylcholinesterase activity / synaptic cleft / side of membrane / chemical synaptic transmission / synapse / protein homodimerization activity / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
Acetylcholinesterase, insect / 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 ...Acetylcholinesterase, insect / 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
Chem-760 / PROPANOIC ACID / Acetylcholinesterase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNachon, F. / Sussman, J.L.
CitationJournal: Molecules / Year: 2020
Title: A Second Look at the Crystal Structures ofDrosophila melanogasterAcetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of ...Title: A Second Look at the Crystal Structures ofDrosophila melanogasterAcetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of Specific Insecticides.
Authors: Nachon, F. / Rosenberry, T.L. / Silman, I. / Sussman, J.L.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionMar 18, 2020ID: 1DX4
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 3.0May 5, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_validate_symm_contact / struct_conn
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_seq_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1187
Polymers64,6541
Non-polymers1,4646
Water2,594144
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,48813
Polymers129,3092
Non-polymers2,17911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)95.810, 95.810, 162.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-604-

SO4

21A-605-

CL

31A-741-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetylcholinesterase / / AChE


Mass: 64654.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ace, CG17907 / Plasmid: S2-SEC 1/3 / Cell line (production host): SCHNEIDER LINE 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07140, acetylcholinesterase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}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.: 1
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, 148 molecules

#3: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-760 / 9-(3-PHENYLMETHYLAMINO)-1,2,3,4-TETRAHYDROACRIDINE / 9-N-PHENYLMETHYLAMINO-TACRINE


Mass: 288.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 13% MPEG2000, 0.1 M ammonium sulfate, 0.03 M leucine, 0.1 M acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: Brandeis B4 / Detector: CCD / Date: Jun 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→29.78 Å / Num. obs: 20596 / % possible obs: 95.98 % / Redundancy: 5 % / Biso Wilson estimate: 50.19 Å2 / Rrim(I) all: 0.038 / Net I/σ(I): 24.3
Reflection shellResolution: 2.7→2.796 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1809 / Rrim(I) all: 0.274

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Processing

Software
NameVersionClassification
XDSdata processing
XSCALEdata scaling
PHASERphasing
PHENIX1.16_3549refinement
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qon

1qon
PDB Unreleased entry


Resolution: 2.7→29.78 Å / SU ML: 0.3542 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9012
RfactorNum. reflection% reflection
Rfree0.2344 2030 9.87 %
Rwork0.1717 --
obs0.178 20577 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.87 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 97 144 4473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784458
X-RAY DIFFRACTIONf_angle_d0.89066069
X-RAY DIFFRACTIONf_chiral_restr0.0565642
X-RAY DIFFRACTIONf_plane_restr0.0062787
X-RAY DIFFRACTIONf_dihedral_angle_d5.443572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.38781350.29841035X-RAY DIFFRACTION84.05
2.76-2.830.32911340.26441167X-RAY DIFFRACTION92.86
2.83-2.910.30971350.24791218X-RAY DIFFRACTION97.06
2.91-2.990.33691190.21411253X-RAY DIFFRACTION97.72
2.99-3.090.31391480.22021232X-RAY DIFFRACTION97.94
3.09-3.20.30361370.21671234X-RAY DIFFRACTION98.14
3.2-3.330.2921160.20351261X-RAY DIFFRACTION98.43
3.33-3.480.24751290.19541251X-RAY DIFFRACTION97.94
3.48-3.660.24931480.16551251X-RAY DIFFRACTION98.31
3.66-3.890.23251150.15531276X-RAY DIFFRACTION98.17
3.89-4.190.20791530.13891253X-RAY DIFFRACTION98.25
4.19-4.610.151360.12361262X-RAY DIFFRACTION97.9
4.61-5.280.17641580.12421256X-RAY DIFFRACTION97.18
5.28-6.640.20891410.15991274X-RAY DIFFRACTION96.32
6.64-29.780.22521260.17261324X-RAY DIFFRACTION91.71
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)
12.49131191739-0.998592563030.9225909989282.58401894613-0.6562137449063.251311642560.06404542027080.4143963316090.0541531782255-0.360018985225-0.197789947970.0632215930557-0.1859023068660.388325263280.1200496116340.2703991981050.03983968894310.007436417841250.3520834207880.003602011784140.25046550927320.433947759665.3097148661-0.391849821428
21.780008887510.4163041139041.856095302232.722683573770.09339248408062.97433651921-0.0394713278562-0.1858839248150.28415670898-0.0477707480742-0.08059300680520.699122467-0.163477840683-0.2426752091510.06773407465210.2403823196780.02104642987730.04561965751970.413948600043-0.03681632078450.50167986857420.117666440861.730826424718.256111257
32.18561488848-0.45217823270.7775168389162.610452872480.5380140338153.5755962385-0.268427902918-0.1763363367230.1377030242030.1126383522190.118145793021-0.329823008934-0.5387003793330.4581529133670.1829598089570.3454221978630.00716516544117-0.0125068232230.3739694690360.03974465137760.2863291589733.225955162366.091593570723.1429812165
42.447487041910.07729379138891.084279687272.17010734244-0.1765018788633.70803477707-0.0950473575897-0.389362849603-0.428667807740.1797753578610.03175110538410.1442065875990.4062690798280.0531957645953-0.02308846768990.2996125980560.01733525054150.0673872461820.2939151274540.1252396428680.32914560887726.137444232551.940603458124.2868438795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 343 )
2X-RAY DIFFRACTION2chain 'A' and (resid 344 through 375 )
3X-RAY DIFFRACTION3chain 'A' and (resid 376 through 499 )
4X-RAY DIFFRACTION4chain 'A' and (resid 500 through 573 )

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