+Open data
-Basic information
Entry | Database: PDB / ID: 3zlq | ||||||
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Title | BACE2 XAPERONE COMPLEX | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / Golgi apparatus / endoplasmic reticulum / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) LAMA GLAMA (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å | ||||||
Authors | Kuglstatter, A. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zlq.cif.gz | 362.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zlq.ent.gz | 309.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zlq ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zlq | HTTPS FTP |
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-Related structure data
Related structure data | 3zmgC 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
#1: Protein | Mass: 42047.355 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR, RESIDUES 75-460 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Z0, memapsin 1 #2: Antibody | Mass: 13152.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli) #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. ...THE PDB FILE IS NUMBERED AFTER PDB-ENTRY 2EWY WHICH HAS NUMBERS 62 LESS THAN THE DATA BANK SEQUENCE. THE MUTATION HERE IS E269A IN THE PDB FILE AND E331A IN THE DATA BANK SEQUENCE. ANTIBODY RAISED IN LLAMA AGAINST BACE2. V(HH) EXPRESSED IN E. COLI. WITH 6HIS AND EPEA TAG. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 25% PEG1500, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→46.26 Å / Num. obs: 67998 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.1→46.26 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.874 / SU B: 15.407 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.261 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.26 Å
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