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- PDB-2zji: Crystal structure of the human BACE1 catalytic domain in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zji | ||||||
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Title | Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(2,6-dimethoxy-benzyl)-piperidin-4-yl]-4-mercapto-butyramide | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE / BACE1 / small-molecule inhibitor / Aspartyl protease / Glycoprotein / Membrane / Protease / Transmembrane / Zymogen | ||||||
Function / homology | ![]() memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / protein processing / recycling endosome / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Randal, M. / Lam, M.B. / Romanowski, M.J. | ||||||
![]() | ![]() Title: Fragment-based discovery of novel BACE1 inhibitors using Tethering technology Authors: Yang, W. / Fucini, R.V. / Fahr, B.T. / Randal, M. / Lind, K.E. / Lam, M.B. / Lu, W. / Lu, Y. / Cary, D.R. / Romanowski, M.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 | ![]() | 93.5 KB | Display | ![]() |
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PDB format | ![]() | 68.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 682.9 KB | Display | ![]() |
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Full document | ![]() | 686.8 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zjhC ![]() 2zjjC ![]() 2zjkC ![]() 2zjlC ![]() 2zjmC ![]() 2zjnC ![]() 2p8hS 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: 45240.930 Da / Num. of mol.: 1 / Fragment: BACE1 catalytic domain, UNP residues 43-446 / Mutation: T329C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-F1I / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 2.0M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 6, 2003 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 24184 / % possible obs: 100 % / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.357 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2P8H Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.071 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.675 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: 74.1225 Å / Origin y: 32.3756 Å / Origin z: 28.2377 Å
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