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- PDB-1ut6: Structure of acetylcholinesterase (E.C. 3.1.1.7) complexed with N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ut6 | ||||||
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Title | Structure of acetylcholinesterase (E.C. 3.1.1.7) complexed with N-9-(1',2',3',4'-Tetrahydroacridinyl)-1,8- diaminooctane at 2.4 angstroms resolution. | ||||||
![]() | ACETYLCHOLINESTERASE | ||||||
![]() | HYDROLASE / SERINE HYDROLASE / ACETYLCHOLINESTERASE / NEUROTRANSMITTER CLEAVAGE / ALZHEIMER'S DISEASE / BIVALENT LIGAND / DUAL-SITE BINDING / INHIBITOR / TACRINE / AMINE / HETERODIMER / SERINE ESTERASE SYNAPSE / MEMBRANE / NERVE / MUSCLE / GPI-ANCHOR NEUROTRANSMITTER DEGRADATION / GLYCOPROTEIN | ||||||
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 | ![]() ![]() | ||||||
![]() | Brumshtein, B. / Wong, D.M. / Greenblatt, H.M. / Carlier, P.R. / Pang, Y.-P. / Silman, I. / Sussman, J.L. | ||||||
![]() | ![]() Title: Complexes of Alkylene-Linked Tacrine Dimers with Torpedo Californica Acetylcholinesterase: Binding of Bis(5)-Tacrine Produces a Dramatic Rearrangement in the Active-Site Gorge. Authors: Rydberg, E.H. / Brumshtein, B. / Greenblatt, H.M. / Wong, D.M. / Shaya, D. / Williams, L.D. / Carlier, P.R. / Pang, Y.-P. / Silman, I. / Sussman, J.L. #1: ![]() Title: Acetylcholinesterase Complexed with Bivalent Ligands Related to Huperzine A: Experimental Evidence for Species-Dependent Protein-Ligand Complementarity Authors: Wong, D.M. / Greenblatt, H.M. / Dvir, H. / Carlier, P.R. / Han, Y.-F. / Pang, Y.-P. / Silman, I. / Sussman, J.L. #2: Journal: J.Med.Chem. / Year: 1999 Title: Heterodimeric Tacrine-Based Acetylcholinesterase Inhibitors: Investigating Ligand-Peripheral Site Interactions Authors: Carlier, P.R. / Chow, E.S.-H. / Han, Y.-F. / Liu, J. / El Yazal, J. / Pang, Y.-P. #3: Journal: J. Comput. Aided Mol. Des. / Year: 1994 Title: Prediction of the Binding Sites of Huperzine a in Acetylcholinesterase by Docking Studies Authors: Pang, Y.-P. / Kozikowski, A.P. #4: ![]() Title: Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase Authors: Harel, M. / Schalk, I. / Ehret-Sabatier, L. / Bouet, F. / Goeldner, M. / Hirth, C. / Axelsen, P.H. / Silman, I. / Sussman, J.L. #5: Journal: Science / Year: 1991 Title: Atomic Structure of Acetylcholinesterase from Torpedo Californica: A Prototypic Acetylcholine-Binding Protein Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.6 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 653.3 KB | Display | ![]() |
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Full document | ![]() | 661.9 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1odcC ![]() 2ckmC ![]() 2cmfC ![]() 2aceS 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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Unit cell |
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Components
#1: Protein | Mass: 60792.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SYNTHETIC HETEROBIVALENT TACRINE-BASED DIMER, A8NH2 (N-9-(1', 2', 3', 4'-TETRAHYDROACRIDINYL)-1, 8-DIAMINOOCTANE) DIHYDROCHLORIDE WITH THE TACRINE MOIETY BOUND TO THE 'ANIONIC' SUBSITE, NEAR ...Details: SYNTHETIC HETEROBIVALENT TACRINE-BASED DIMER, A8NH2 (N-9-(1', 2', 3', 4'-TETRAHYDROACRIDINYL)-1, 8-DIAMINOOCTANE) DIHYDROCHLORIDE WITH THE TACRINE MOIETY BOUND TO THE 'ANIONIC' SUBSITE, NEAR THE BOTTOM OF THE ACTIVE SITE GORGE, AND THE 8-AMINO MOIETY BOUND TO THE 'PERIPHERAL' ANIONIC SITE (PAS) AT THE TOP OF THE GORGE OF TCACHE. THE LIGAND, A8NH2, THUS BINDS BY SPANNING THE ACTIVE-SITE GORGE. Source: (natural) ![]() ![]() Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase | ||||||||
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#2: Sugar | #3: Chemical | ChemComp-A8N / | #4: Water | ChemComp-HOH / | Compound details | PROTEIN HYDROLYZES | Sequence details | THE SEQUENCE DESCRIBED BELOW IS THAT OF THE T-ISOFORM SPLICE VARIANT OF SWISSPROT ENTRY P04058 AND ...THE SEQUENCE DESCRIBED BELOW IS THAT OF THE T-ISOFORM SPLICE VARIANT OF SWISSPROT ENTRY P04058 AND ANNOTATED IN FTID=VSP_001460 GLU A 536 SWS P04058 ALA 557 THR A 537 SWS P04058 CYS 558 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.56 % |
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Crystal grow | Temperature: 277 K / pH: 5.8 Details: PROTEIN WAS CRYSTALLISED FROM 28-33% V/V PEG 200 0.5M MES PH 5.8 AT 4 DEG. CELSIUS; THEN SOAKED IN MOTHER LIQUOR (40% V/V PEG 200 IN 0.1 M MES BUFFER, PH 5.8) CONTAINING 2MM N-9-(1',2',3',4'- ...Details: PROTEIN WAS CRYSTALLISED FROM 28-33% V/V PEG 200 0.5M MES PH 5.8 AT 4 DEG. CELSIUS; THEN SOAKED IN MOTHER LIQUOR (40% V/V PEG 200 IN 0.1 M MES BUFFER, PH 5.8) CONTAINING 2MM N-9-(1',2',3',4'-TETRAHYDROACRIDINYL) -1,8-DIAMINOOCTANE BIS-HYDROCHLORIDE (A8NH2.2HCL) |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 18, 2001 / Details: OSMIC BLUE CONFOCAL MIRRO |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 38785 / % possible obs: 97 % / Redundancy: 3.22 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.95 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.44 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ACE Resolution: 2.4→29.14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1843636.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE ASP A1, ASP A2, HIS A3 AND THE C-TERMINAL RESIDUES AFTER THR A535. SEVERAL RESIDUES MISSING IN CHAIN ...Details: SEVERAL RESIDUES ARE NOT SEEN IN THE CRYSTAL STRUCTURE, DUE TO DISORDER. THESE INCLUDE ASP A1, ASP A2, HIS A3 AND THE C-TERMINAL RESIDUES AFTER THR A535. SEVERAL RESIDUES MISSING IN CHAIN BREAK, FROM HIS A486 - GLU A489 (INCLUSIVE).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.7999 Å2 / ksol: 0.351354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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