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Open data
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Basic information
Entry | Database: PDB / ID: 4ivs | ||||||
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Title | Crystal structure of BACE1 with its inhibitor | ||||||
![]() | Beta-secretase 1![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Chen, T.T. / Li, L. / Chen, W.Y. / Xu, Y.C. | ||||||
![]() | ![]() Title: Virtual screening and structure-based discovery of indole acylguanidines as potent beta-secretase (BACE1) inhibitors Authors: Zou, Y. / Li, L. / Chen, W.Y. / Chen, T.T. / Ma, L. / Wang, X. / Xiong, B. / Xu, Y.C. / Shen, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ivtC ![]() 2b8lS 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: 48222.922 Da / Num. of mol.: 1 / Fragment: UNP residues 43-454 / Mutation: K75A, E77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-VSI / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.85 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.6M Li2SO4, 100mM HEPES, 25% PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 131109 / Rmerge(I) obs: 0.137 / D res high: 2.5 Å / Num. obs: 35192 / % possible obs: 99.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.4→43.39 Å / Num. obs: 39572 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.82 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 12.89 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2B8L Resolution: 2.636→43.388 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8491 / SU ML: 0.25 / σ(F): 2.02 / Phase error: 21.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.44 Å2 / Biso mean: 25.8459 Å2 / Biso min: 8.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.636→43.388 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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