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- PDB-3i6z: 3D Structure of Torpedo californica acetylcholinesterase complexe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i6z | |||||||||
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Title | 3D Structure of Torpedo californica acetylcholinesterase complexed with N-saccharinohexyl-galanthamine | |||||||||
![]() | Acetylcholinesterase | |||||||||
![]() | HYDROLASE / 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 | ![]() acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lamba, D. / Bartolucci, C. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.3 KB | Display | ![]() |
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PDB format | ![]() | 99.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i6mC ![]() 1ea5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60447.211 Da / Num. of mol.: 1 / Fragment: UNP residues 23-556 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P04058, acetylcholinesterase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-G6X / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 42% PEG200, 100mM MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 9, 2001 / Details: Three-segment Pt-coated toroidal mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→19.91 Å / Num. all: 50750 / Num. obs: 50534 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.037 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.19→2.28 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 5013 / Rsym value: 0.269 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EA5 Resolution: 2.19→19.91 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2049729.49 / Isotropic thermal model: Restrained individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent modeling method used: Flat model
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 88.61 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.19→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.33 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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