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- PDB-3i6m: 3D Structure of Torpedo californica acetylcholinesterase complexe... -

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Basic information

Entry
Database: PDB / ID: 3i6m
Title3D Structure of Torpedo californica acetylcholinesterase complexed with N-piperidinopropyl-galanthamine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Serine hydrolase / Cholinesterase / Neurotransmitter degradation / Alzheimer's disease / Bis-functional galanthamine derivative / Alternative splicing / Cell junction / Cell membrane / Disulfide bond / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Serine esterase / Synapse
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-G3X / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLamba, D. / Bartolucci, C.
Citation
Journal: J.Med.Chem. / Year: 2010
Title: Probing Torpedo californica acetylcholinesterase catalytic gorge with two novel bis-functional galanthamine derivatives.
Authors: Bartolucci, C. / Haller, L.A. / Jordis, U. / Fels, G. / Lamba, D.
#1: Journal: J.Am.Chem.Soc. / Year: 2004
Title: The complex of a bivalent derivative of galanthamine with Torpedo acetylcholinesterase displays drastic deformation of the active-site gorge: implications for structure-based drug design
Authors: Greenblatt, H.M. / Guillou, C. / Guenard, D. / Argaman, A. / Botti, S. / Badet, B. / Thal, C. / Silman, I. / Sussman, J.L.
#2: Journal: FEBS Lett. / Year: 1999
Title: Structure of acetylcholinesterase complexed with (-)-galanthamine at 2.3A resolution
Authors: Greenblatt, H.M. / Kryger, G. / Lewis, T. / Silman, I. / Sussman, J.L.
#3: Journal: PROTEINS / Year: 2001
Title: Three-dimensional structure of a complex of galanthamine (Nivalin) with acetylcholinesterase from Torpedo californica: implications for the design of new anti-Alzheimer drugs
Authors: Bartolucci, C. / Perola, E. / Pilger, C. / Fels, G. / Lamba, D.
#4: Journal: J.MOL.GRAPH.MODEL. / Year: 2001
Title: Accurate prediction of the bound conformation of galanthamine in the active site of Torpedo californica acetylcholinesterase using molecular docking
Authors: Pilger, C. / Bartolucci, C. / Lamba, D. / Tropsha, A. / Fels, G.
#5: Journal: J.Mol.Model. / Year: 2002
Title: Galanthamine as bis-functional ligand for the acetylcholinesterase.
Authors: Luttmann, E. / Linnemann, E. / Fels, G.
#6: Journal: J.Chem.Inf.Model. / Year: 2006
Title: A QXP-based multistep docking procedure for accurate prediction of protein-ligand complexes
Authors: Alisaraie, L. / Fels, G.
History
DepositionJul 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
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_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4914
Polymers60,4471
Non-polymers1,0443
Water7,170398
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9838
Polymers120,8942
Non-polymers2,0886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2900 Å2
ΔGint3 kcal/mol
Surface area39760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.194, 112.194, 137.194
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-G3X / (4aS,6R,8aS)-3-methoxy-11-(3-piperidin-1-ylpropyl)-5,6,9,10,11,12-hexahydro-4aH-[1]benzofuro[3a,3,2-ef][2]benzazepin-6-ol / (4aS,6R,8aS)-4a,5,9,10,11,12-Hexahydro-3-methoxy-11-[3-(1-piperidinyl)propyl]-6H-benzofuro[3a,3,2-ef][2]benzazepin-6-ol


Mass: 398.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 4.12 Å3/Da / Density % sol: 70.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 42% PEG200, 100mM MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2001 / Details: Three-segment Pt-coated toroidal mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→19.82 Å / Num. all: 47210 / Num. obs: 46878 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 8.8
Reflection shellResolution: 2.26→2.28 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 957 / Rsym value: 0.418 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EA5

1ea5


Resolution: 2.26→19.82 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1997132.14 / Isotropic thermal model: Restrained individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4701 10 %Random
Rwork0.18 ---
all0.18 46874 --
obs0.18 46822 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.8 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.3 Å28.3 Å2-16.6 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.26→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 71 398 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it2.7331.5
X-RAY DIFFRACTIONc_mcangle_it3.5252
X-RAY DIFFRACTIONc_scbond_it4.7892
X-RAY DIFFRACTIONc_scangle_it5.9082.5
LS refinement shellResolution: 2.26→2.33 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 397 10 %
Rwork0.242 3572 -
obs--46.6 %

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