+Open data
-Basic information
Entry | Database: PDB / ID: 6ej2 | ||||||
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Title | BACE1 compound 28 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / BACE1 / protease / Alzheimer | ||||||
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 / prepulse inhibition / amyloid-beta metabolic process ...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 / prepulse inhibition / amyloid-beta metabolic process / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / 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 / amyloid-beta binding / peptidase activity / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / 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: 1.46 Å | ||||||
Authors | Johansson, P. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Toward beta-Secretase-1 Inhibitors with Improved Isoform Selectivity. Authors: Johansson, P. / Kaspersson, K. / Gurrell, I.K. / Back, E. / Eketjall, S. / Scott, C.W. / Cebers, G. / Thorne, P. / McKenzie, M.J. / Beaton, H. / Davey, P. / Kolmodin, K. / Holenz, J. / ...Authors: Johansson, P. / Kaspersson, K. / Gurrell, I.K. / Back, E. / Eketjall, S. / Scott, C.W. / Cebers, G. / Thorne, P. / McKenzie, M.J. / Beaton, H. / Davey, P. / Kolmodin, K. / Holenz, J. / Duggan, M.E. / Budd Haeberlein, S. / Burli, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ej2.cif.gz | 167.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ej2.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 6ej2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6ej2 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6ej2 | 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: 55815.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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: Chemical | ChemComp-B7E / |
#3: 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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18% PEG 5k MME, 0.2M AmI, 0.2M sodium citrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→48.68 Å / Num. obs: 88595 / % possible obs: 97.9 % / Redundancy: 9 % / Biso Wilson estimate: 27.93 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.46→1.51 Å / Rmerge(I) obs: 1.015 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→48.68 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9421 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.075
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Displacement parameters | Biso mean: 36.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.259 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.46→48.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.5 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -15.0925 Å / Origin y: -40.917 Å / Origin z: 0.3879 Å
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Refinement TLS group | Selection details: { A|* } |