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Open data
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Basic information
Entry | Database: PDB / ID: 3tpp | ||||||
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Title | Crystal structure of BACE1 complexed with an inhibitor | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / MEMAPSIN 2 / PROTEASE / BACE1 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / recycling endosome / protein processing / 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 | ![]() ![]() ![]() | ||||||
![]() | Xu, Y.C. / Li, M.J. / Greenblatt, H. / Chen, T.T. / Silman, I. / Sussman, J.L. | ||||||
![]() | ![]() Title: Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations Authors: Xu, Y.C. / Li, M.J. / Greenblatt, H. / Chen, W.Y. / Paz, A. / Dym, O. / Peleg, Y. / Chen, T.T. / Shen, X. / He, J.H. / Jiang, H.L. / Silman, I. / Sussman, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104 KB | Display | ![]() |
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PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.6 KB | Display | ![]() |
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Full document | ![]() | 841.8 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tpjC ![]() 3tplC ![]() 3tprC ![]() 2qp8S 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 353 molecules ![](data/chem/img/5HA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-5HA / | ||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-URE / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5-1.8M Li2SO4, 100mM HEPES, 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→81 Å / Num. obs: 68069 / Observed criterion σ(I): 2.91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QP8 Resolution: 1.6→43.166 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 15.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.585 Å2 / ksol: 0.393 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.56 Å2 / Biso mean: 15.2153 Å2 / Biso min: 4.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→43.166 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: 24
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