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Yorodumi- PDB-3vf3: Crystal Structure of Human Beta Secretase in Complex with NVP-BQQ711 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vf3 | ||||||
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Title | Crystal Structure of Human Beta Secretase in Complex with NVP-BQQ711 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / Structure-based drug design / 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 / 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 / late endosome / synaptic vesicle / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 Å | ||||||
Authors | Rondeau, J.M. / Bourgier, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Discovery of cyclic sulfone hydroxyethylamines as potent and selective beta-site APP-cleaving enzyme 1 (BACE1) inhibitors: structure based design and in vivo reduction of amyloid beta-peptides Authors: Rueeger, H. / Lueoend, R. / Rogel, O. / Rondeau, J.M. / Mobitz, H. / Machauer, R. / Jacobson, L. / Staufenbiel, M. / Desrayaud, S. / Neumann, U. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors. Authors: Rueeger, H. / Rondeau, J.M. / McCarthy, C. / Mobitz, H. / Tintelnot-Blomley, M. / Neumann, U. / Desrayaud, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vf3.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vf3.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vf3_validation.pdf.gz | 754.4 KB | Display | wwPDB validaton report |
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Full document | 3vf3_full_validation.pdf.gz | 756.6 KB | Display | |
Data in XML | 3vf3_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 3vf3_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vf3 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vf3 | HTTPS FTP |
-Related structure data
Related structure data | 3veuC 3vg1C 4d83C 4d85C 4d88C 4d89C 4d8cC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44777.336 Da / Num. of mol.: 1 / Fragment: unp residues 48-447 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-0GS / ( |
#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: 2.13 Å3/Da / Density % sol: 42.31 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15% PEG 1,500, in water, pH 5.5, vapor diffusion, hanging drop, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2008 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→60.71 Å / Num. all: 61648 / Num. obs: 61648 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.88 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.48→52.22 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8867 / Data cutoff high absF: 1587662 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.9616 Å2 / ksol: 0.3817 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.78 Å2 / Biso mean: 19.8196 Å2 / Biso min: 7.71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.48→52.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.57 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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