[English] 日本語
![](img/lk-miru.gif)
- PDB-6jsz: BACE2 xaperone complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jsz | ||||||
---|---|---|---|---|---|---|---|
Title | BACE2 xaperone complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide | ||||||
![]() |
| ||||||
![]() | HYDROLASE/IMMUNE SYSTEM / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujimoto, K. / Matsuoka, E. / Asada, N. / Tadano, G. / Yamamoto, T. / Nakahara, K. / Fuchino, K. / Ito, H. / Kanegawa, N. / Moechars, D. ...Fujimoto, K. / Matsuoka, E. / Asada, N. / Tadano, G. / Yamamoto, T. / Nakahara, K. / Fuchino, K. / Ito, H. / Kanegawa, N. / Moechars, D. / Gijsen, H.J.M. / Kusakabe, K.I. | ||||||
![]() | ![]() Title: Structure-Based Design of Selective beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors: Targeting the Flap to Gain Selectivity over BACE2. Authors: Fujimoto, K. / Matsuoka, E. / Asada, N. / Tadano, G. / Yamamoto, T. / Nakahara, K. / Fuchino, K. / Ito, H. / Kanegawa, N. / Moechars, D. / Gijsen, H.J.M. / Kusakabe, K.I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 115.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6jseC ![]() 6jsfC ![]() 6jsgC ![]() 6jsnC ![]() 3zkgS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | ![]() Mass: 42105.391 Da / Num. of mol.: 1 / Mutation: AEPLC, ALP56, ASP21 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 11769.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-C7O / |
#4: Chemical | ChemComp-CL / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % / Description: NONE |
---|---|
Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M TRIS pH 8.0, 25% PEG 3350, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.53→61.51 Å / Num. obs: 78375 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rrim(I) all: 0.04 / Rsym value: 0.035 / Net I/σ(I): 19.09 |
Reflection shell | Resolution: 1.53→1.78 Å / Redundancy: 4.1 % / Num. unique obs: 28173 / Rrim(I) all: 0.563 / Rsym value: 0.49 / % possible all: 99.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 3ZKG Resolution: 1.53→61.51 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.251 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.085 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.57 Å2 / Biso mean: 28.96 Å2 / Biso min: 15.92 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→61.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.531→1.571 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|