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Yorodumi- PDB-1gpk: Structure of Acetylcholinesterase Complex with (+)-Huperzine A at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gpk | |||||||||
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Title | Structure of Acetylcholinesterase Complex with (+)-Huperzine A at 2.1A Resolution | |||||||||
Components | ACETYLCHOLINESTERASE | |||||||||
Keywords | HYDROLASE / CHOLINESTERASE / HUPERZINE A / ALZHEIMER'S DISEASE | |||||||||
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 | |||||||||
Biological species | TORPEDO CALIFORNICA (Pacific electric ray) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Dvir, H. / Harel, M. / Chetrit, M. / Silman, I. / Sussman, J.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpk.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpk.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpk ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpk | HTTPS FTP |
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-Related structure data
Related structure data | 1ea5SC 1gpnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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) TORPEDO CALIFORNICA (Pacific electric ray) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |