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Yorodumi- PDB-5f00: CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-[3-[(3-chloro-8-qui... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f00 | ||||||
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Title | CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-[3-[(3-chloro-8-quinolyl)amino]phenyl]-5-methyl-2,6-dihydro-1,4-oxazin-3-amine | ||||||
Components | Beta-secretase 1 | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Banner, D. / Benz, J. / Stihle, M. / Kuglstatter, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: A Real-World Perspective on Molecular Design. Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f00.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f00.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 5f00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f00 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f00 | HTTPS FTP |
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-Related structure data
Related structure data | 5edbC 5edcC 5edeC 5edgC 5edhC 5ediC 5ezxC 5ezzC 5f01C 5f02C 5f03C 5i2rC 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: 43411.895 Da / Num. of mol.: 1 / Mutation: K307A 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 | #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-5T8 / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5M SODIUM FORMATE, 100MM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.82 Å / Num. obs: 36938 / % possible obs: 99.5 % / Redundancy: 11.3 % / Rsym value: 0.0413 / Net I/σ(I): 20.49 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 10.72 % / Rmerge(I) obs: 0.3744 / Mean I/σ(I) obs: 2.79 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→44.82 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.332 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.896 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→44.82 Å
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