+Open data
-Basic information
Entry | Database: PDB / ID: 3zmg | ||||||
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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 / cellular response to manganese ion / prepulse inhibition / 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 / cellular response to manganese ion / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / 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 / 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: 1.74 Å | ||||||
Authors | Banner, D.W. / Kuglstatter, A. / Benz, J. / Stihle, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Beta-Secretase (Bace1) Inhibitors with High in Vivo Efficacy Suitable for Clinical Evaluation in Alzheimer'S Disease. Authors: Hilpert, H. / Guba, W. / Woltering, T.J. / Wostl, W. / Pinard, E. / Mauser, H. / Mayweg, A.V. / Rogers-Evans, M. / Humm, R. / Krummenacher, D. / Muser, T. / Schnider, C. / Jacobsen, H. / ...Authors: Hilpert, H. / Guba, W. / Woltering, T.J. / Wostl, W. / Pinard, E. / Mauser, H. / Mayweg, A.V. / Rogers-Evans, M. / Humm, R. / Krummenacher, D. / Muser, T. / Schnider, C. / Jacobsen, H. / Ozmen, L. / Bergadano, A. / Banner, D.W. / Hochstrasser, R. / Kuglstatter, A. / David-Pierson, P. / Fischer, H. / Polara, A. / 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 | 3zmg.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zmg.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/3zmg ftp://data.pdbj.org/pub/pdb/validation_reports/zm/3zmg | HTTPS FTP |
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-Related structure data
Related structure data | 3zlqC 4j0pC 4j0tC 4j0vC 4j0yC 4j0zC 4j17C 4j1cC 4j1eC 4j1fC 4j1hC 4j1iC 4j1kC 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 on special symmetry positions |
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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-6Z0 / | ||||
#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: 2.87 Å3/Da / Density % sol: 57.3 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 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: 1.0007 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→49.12 Å / Num. obs: 55318 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.08 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.27 |
Reflection shell | Resolution: 1.74→1.84 Å / Redundancy: 13.26 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.78 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN HOUSE STRUCTURES Resolution: 1.74→49.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.273 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT NOT OUTPUT. U VALUES REFINED INDIVIDUALLY.
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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: 25.845 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→49.12 Å
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