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- PDB-3dv1: Crystal structure of human beta-secretase in complex with NVP-ARV999 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dv1 | ||||||
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Title | Crystal structure of human beta-secretase in complex with NVP-ARV999 | ||||||
![]() | Beta-secretase 1![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rondeau, J.-M. | ||||||
![]() | ![]() Title: Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo. Authors: Machauer, R. / Laumen, K. / Veenstra, S. / Rondeau, J.M. / Tintelnot-Blomley, M. / Betschart, C. / Jaton, A.L. / Desrayaud, S. / Staufenbiel, M. / Rabe, S. / Paganetti, P. / Neumann, U. #1: ![]() Title: Structure-based design and synthesis of macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors. Authors: Machauer, R. / Veenstra, S. / Rondeau, J.M. / Tintelnot-Blomley, M. / Betschart, C. / Neumann, U. / Paganetti, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.9 KB | Display | ![]() |
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PDB format | ![]() | 197.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dv5C ![]() 3duyS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 44777.336 Da / Num. of mol.: 3 / Fragment: Catalytic domain: Residues 48-447 Source method: isolated from a genetically manipulated source Details: Refolded / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.69 % |
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Crystal grow![]() | Details: 1.0M Ammonium sulfate in water, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K. Protein stock was BACE 7.3 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl. Crystals were grown in 96-well ...Details: 1.0M Ammonium sulfate in water, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K. Protein stock was BACE 7.3 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl. Crystals were grown in 96-well Corning Microtiter plates. Cryo-protectant was 80% well solution, 20% 1,2-Propanediol |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→100 Å / Num. all: 93176 / Num. obs: 93176 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.004 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.309 / Num. unique all: 9252 / Χ2: 0.47 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3DUY Resolution: 2.1→55.52 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.829 / Data cutoff high absF: 17397696 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.539 Å2 / ksol: 0.344 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.07 Å2 / Biso mean: 46.843 Å2 / Biso min: 20.28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→55.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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