+Open data
-Basic information
Entry | Database: PDB / ID: 3buf | ||||||
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Title | BACE-1 complexed with compound 2 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / ALZHEIMER'S DISEASE / ASPARTIC PROTEASE / BETA-SECRETASE / MEMAPSIN 2 / FRAGMENT SCREEN / ALTERNATIVE SPLICING / ASPARTYL PROTEASE / GLYCOPROTEIN / MEMBRANE / TRANSMEMBRANE / ZYMOGEN | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Kuglstatter, A. / Hennig, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Tyramine fragment binding to BACE-1 Authors: Kuglstatter, A. / Stahl, M. / Peters, J.U. / Huber, W. / Stihle, M. / Schlatter, D. / Benz, J. / Ruf, A. / Roth, D. / Enderle, T. / Hennig, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3buf.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3buf.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 3buf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3buf ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3buf | 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
#1: Protein | Mass: 45554.008 Da / Num. of mol.: 1 / Fragment: protease domain / Mutation: K246A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-AEG / |
#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: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.5M SODIUM FORMATE, 100MM HEPES, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95 |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 23631 / % possible obs: 97.6 % / Rsym value: 0.074 / Net I/σ(I): 22.86 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.98 / Rsym value: 0.508 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→49.39 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 42.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å
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