+Open data
-Basic information
Entry | Database: PDB / ID: 5mbw | ||||||
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Title | CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH Pep#3 | ||||||
Components |
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Keywords | HYDROLASE / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 / 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 / lysosome / aspartic-type endopeptidase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Kuglstatter, A. / Stihle, M. / Benz, J. | ||||||
Citation | Journal: EBioMedicine / Year: 2017 Title: Potent and Selective BACE-1 Peptide Inhibitors Lower Brain A beta Levels Mediated by Brain Shuttle Transport. Authors: Ruderisch, N. / Schlatter, D. / Kuglstatter, A. / Guba, W. / Huber, S. / Cusulin, C. / Benz, J. / Rufer, A.C. / Hoernschemeyer, J. / Schweitzer, C. / Bulau, T. / Gartner, A. / Hoffmann, E. / ...Authors: Ruderisch, N. / Schlatter, D. / Kuglstatter, A. / Guba, W. / Huber, S. / Cusulin, C. / Benz, J. / Rufer, A.C. / Hoernschemeyer, J. / Schweitzer, C. / Bulau, T. / Gartner, A. / Hoffmann, E. / Niewoehner, J. / Patsch, C. / Baumann, K. / Loetscher, H. / Kitas, E. / Freskgard, P.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mbw.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mbw.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 5mbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/5mbw ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mbw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45612.109 Da / Num. of mol.: 1 / Mutation: K307A Source method: isolated from a genetically manipulated source Details: Engineered mutation / Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2 |
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#2: Protein/peptide | Mass: 1411.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Please see uploaded gif file. / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.66 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium chloride, 0.1M HEPES, 1.6M ammonium sulfate, 0.098M HEGA-9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→47.45 Å / Num. obs: 1554 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.996 / Rpim(I) all: 0.073 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.95→3.13 Å / Redundancy: 21 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.545 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 28.15 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.3
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.289 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→47.45 Å
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