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Yorodumi- PDB-2zjk: Crystal structure of the human BACE1 catalytic domain in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zjk | ||||||
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Title | Crystal structure of the human BACE1 catalytic domain in complex with 4-(4-fluoro-benzyl)-piperazine-2-carboxylic acid(3-mercapto-propyl)-amide | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / BACE1 / small-molecule inhibitor / Tethering / Alternative splicing / Aspartyl protease / Glycoprotein / Membrane / Protease / Transmembrane / Zymogen | ||||||
Function / homology | Function and homology information 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 / multivesicular body / hippocampal mossy fiber to CA3 synapse / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / aspartic-type endopeptidase activity / amyloid fibril formation / endosome / endosome membrane / early endosome / lysosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / enzyme binding / cell surface / Golgi apparatus / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Randal, M. / Lam, M.B. / Lu, W. / Romanowski, M.J. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zjk.cif.gz | 224.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zjk.ent.gz | 180.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zjk_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2zjk_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2zjk_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2zjk_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/2zjk ftp://data.pdbj.org/pub/pdb/validation_reports/zj/2zjk | HTTPS FTP |
-Related structure data
Related structure data | 2zjhC 2zjiC 2zjjC 2zjlC 2zjmC 2zjnC 2p8hS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: F1K / End label comp-ID: F1K / Refine code: 1 / Auth seq-ID: 1 - 449 / Label seq-ID: 21
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-Components
#1: Protein | Mass: 45240.930 Da / Num. of mol.: 3 / Fragment: BACE1 catalytic domain, UNP residues 43-446 / Mutation: T72C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P56817, memapsin 2 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Bis-Tris pH 5.5, 0.2M lithium sulfate monohydrate, 25% w/v polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 24, 2004 |
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: 2.8→20 Å / Num. all: 101873 / Num. obs: 37401 / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.555 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2P8H Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.875 / SU B: 24.187 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / 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: 65.905 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.103 Å / Total num. of bins used: 15
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