+Open data
-Basic information
Entry | Database: PDB / ID: 4bek | ||||||
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Title | CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH CHEMICAL LIGAND | ||||||
Components | BETA-SECRETASE 1 | ||||||
Keywords | HYDROLASE | ||||||
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 / amyloid-beta metabolic process / cellular response to manganese ion / detection of mechanical stimulus involved in sensory perception of pain ...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 / amyloid-beta metabolic process / cellular response to manganese ion / detection of mechanical stimulus involved in sensory perception of pain / prepulse inhibition / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / multivesicular body / hippocampal mossy fiber to CA3 synapse / response to lead ion / trans-Golgi network / protein processing / recycling endosome / 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 / early endosome / lysosome / 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 / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Banner, D.W. / Benz, J. / Stihle, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Bace1 Inhibitors: A Head Group Scan on a Series of Amides. Authors: Woltering, T.J. / Wostl, W. / Hilpert, H. / Rogers-Evans, M. / Pinard, E. / Mayweg, A. / Gobel, M. / Banner, D.W. / Benz, J. / Travagli, M. / Pollastrini, M. / Marconi, G. / Gabellieri, E. / ...Authors: Woltering, T.J. / Wostl, W. / Hilpert, H. / Rogers-Evans, M. / Pinard, E. / Mayweg, A. / Gobel, M. / Banner, D.W. / Benz, J. / Travagli, M. / Pollastrini, M. / Marconi, G. / Gabellieri, E. / Guba, W. / Mauser, H. / Andreini, M. / Jacobsen, H. / Power, E. / Narquizian, R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bek.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bek.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bek_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 4bek_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 4bek_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4bek_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/4bek ftp://data.pdbj.org/pub/pdb/validation_reports/be/4bek | HTTPS FTP |
-Related structure data
Related structure data | 4bfdC 3zmgS S: Starting model for refinement 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: 45554.008 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 46-454 / Mutation: YES 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-XK0 / ( | ||||
#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: 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: 3.16 Å3/Da / Density % sol: 61.2 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: CRYSTALLIZATION CONDITIONS: 2.5M SODIUM FORMATE, 100MM HEPES, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→44.86 Å / Num. obs: 21558 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 14.12 % / Biso Wilson estimate: 55.95 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.85 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 13.38 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.65 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZMG Resolution: 2.39→44.86 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.22 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.226 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→44.86 Å
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