+Open data
-Basic information
Entry | Database: PDB / ID: 6bfd | ||||||
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Title | BACE crystal structure with hydroxy pyrrolidine inhibitor | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / BACE1 / beta-secretase / inhibitor / protease / HYDROLASE / 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 / Resolution: 1.62 Å | ||||||
Authors | Timm, D.E. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Optimization of Hydroxyethylamine Transition State Isosteres as Aspartic Protease Inhibitors by Exploiting Conformational Preferences. Authors: Bueno, A.B. / Agejas, J. / Broughton, H. / Dally, R. / Durham, T.B. / Espinosa, J.F. / Gonzalez, R. / Hahn, P.J. / Marcos, A. / Rodriguez, R. / Sanz, G. / Soriano, J.F. / Timm, D. / Vidal, P. ...Authors: Bueno, A.B. / Agejas, J. / Broughton, H. / Dally, R. / Durham, T.B. / Espinosa, J.F. / Gonzalez, R. / Hahn, P.J. / Marcos, A. / Rodriguez, R. / Sanz, G. / Soriano, J.F. / Timm, D. / Vidal, P. / Yang, H.C. / McCarthy, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bfd.cif.gz | 191.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bfd.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/6bfd ftp://data.pdbj.org/pub/pdb/validation_reports/bf/6bfd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48970.117 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 276 K / Method: vapor diffusion, hanging drop Details: 16% PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 127386 / % possible obs: 97.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.28 Å2 / Net I/σ(I): 15.4 |
-Processing
Software |
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Refinement | Resolution: 1.62→45.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.081 / SU Rfree Cruickshank DPI: 0.077
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Displacement parameters | Biso mean: 21.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.62→45.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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