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- PDB-1gpk: Structure of Acetylcholinesterase Complex with (+)-Huperzine A at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gpk | |||||||||
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Title | Structure of Acetylcholinesterase Complex with (+)-Huperzine A at 2.1A Resolution | |||||||||
![]() | ACETYLCHOLINESTERASE | |||||||||
![]() | HYDROLASE / CHOLINESTERASE / HUPERZINE A / ALZHEIMER'S DISEASE | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Dvir, H. / Harel, M. / Chetrit, M. / Silman, I. / Sussman, J.L. | |||||||||
![]() | ![]() Title: X-Ray Structures of Torpedo Californica Acetylcholinesterase Complexed with (+)-Huperzine a and (-)-Huperzine B: Structural Evidence for an Active Site Rearrangement Authors: Dvir, H. / Jiang, H.L. / Wong, D.M. / Harel, M. / Chetrit, M. / He, X.C. / Jin, G.Y. / Yu, G.L. / Tang, X.C. / Silman, I. / Bai, D.L. / Sussman, J.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.8 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 816 KB | Display | ![]() |
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Full document | ![]() | 822.1 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 41.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ea5SC ![]() 1gpnC S: Starting model for refinement C: citing same article ( |
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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: 60736.516 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-558 / Source method: isolated from a natural source / Details: PURIFIED FROM THE ELECTRIC ORGAN Source: (natural) ![]() ![]() Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / 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 | #4: Chemical | ChemComp-HUP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 66.6 % / Description: DATA WERE COLLECTED USING THE ROTATION METHOD | ||||||||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.80 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Raves, M.L., (1997) Nature Struct. Biol., 4, 57. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRUKER-AXS / Detector: CCD / Date: May 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 67270 / % possible obs: 98.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. all: 67270 / Num. obs: 57502 / Num. measured all: 677200 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.416 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EA5 Resolution: 2.1→20 Å / Data cutoff high absF: 1000 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.11 Å / Total num. of bins used: 50
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.006 |