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- PDB-4x3c: TORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH A TACRIN... -

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Basic information

Entry
Database: PDB / ID: 4x3c
TitleTORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH A TACRINE-NICOTINAMIDE HYBRID INHIBITOR
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / multitarget drug / enzyme-inhibitor complex / tacrine / nicotinamide
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / 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, fish/snake / 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-TNH / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPesaresi, A. / Lamba, D.
CitationJournal: To Be Published
Title: TORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH A TACRINE-NICOTINAMIDE HYBRID INHIBITOR
Authors: Pesaresi, A. / Lamba, D.
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 3.0May 12, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact
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_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 3.1Jan 10, 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)61,4954
Polymers60,4471
Non-polymers1,0483
Water3,315184
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9918
Polymers120,8942
Non-polymers2,0966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_767-x+2,-x+y+1,-z+7/31
Buried area2960 Å2
ΔGint2 kcal/mol
Surface area40490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.020, 112.020, 136.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 60447.211 Da / Num. of mol.: 1 / Fragment: UNP residues 23-556 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
References: UniProt: P04058, acetylcholinesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 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
#4: Chemical ChemComp-TNH / N-[6-(1,2,3,4-tetrahydroacridin-9-ylamino)hexyl]pyridine-3-carboxamide / 2-{2-[(1,2,3,4-tetrahydroacridin- 9-yl)amino]hexyl}N-nicotinamide


Mass: 402.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 30% PEG 200, 100mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→39.57 Å / Num. obs: 30872 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 6.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.9 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLM7.0.7data reduction
SCALA3.3.2.1data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA5

1ea5


Resolution: 2.6→39.57 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.848 / SU B: 10.685 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27987 1555 5 %RANDOM
Rwork0.21942 ---
obs0.2224 29275 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.98 Å2-0 Å2
2--0.98 Å2-0 Å2
3----3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 72 184 4519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194468
X-RAY DIFFRACTIONr_bond_other_d0.0020.024110
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9596070
X-RAY DIFFRACTIONr_angle_other_deg0.9053.0049446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71224.038213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28915708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4751524
X-RAY DIFFRACTIONr_chiral_restr0.10.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021088
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5452.3372135
X-RAY DIFFRACTIONr_mcbond_other1.5392.3352134
X-RAY DIFFRACTIONr_mcangle_it2.4933.5022667
X-RAY DIFFRACTIONr_mcangle_other2.4953.5052668
X-RAY DIFFRACTIONr_scbond_it2.0812.6032333
X-RAY DIFFRACTIONr_scbond_other2.082.6042334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4343.8163404
X-RAY DIFFRACTIONr_long_range_B_refined5.33419.3195365
X-RAY DIFFRACTIONr_long_range_B_other5.25219.3045333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 126 -
Rwork0.338 2091 -
obs--97.67 %

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