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Yorodumi- PDB-4djv: Structure of BACE Bound to 2-imino-5-(3'-methoxy-[1,1'-biphenyl]-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4djv | ||||||
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Title | Structure of BACE Bound to 2-imino-5-(3'-methoxy-[1,1'-biphenyl]-3-yl)-3-methyl-5-phenylimidazolidin-4-one | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / BACE1 / Alzheimers / 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 / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Strickland, C. / Cumming, J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor. Authors: Cumming, J.N. / Smith, E.M. / Wang, L. / Misiaszek, J. / Durkin, J. / Pan, J. / Iserloh, U. / Wu, Y. / Zhu, Z. / Strickland, C. / Voigt, J. / Chen, X. / Kennedy, M.E. / Kuvelkar, R. / Hyde, ...Authors: Cumming, J.N. / Smith, E.M. / Wang, L. / Misiaszek, J. / Durkin, J. / Pan, J. / Iserloh, U. / Wu, Y. / Zhu, Z. / Strickland, C. / Voigt, J. / Chen, X. / Kennedy, M.E. / Kuvelkar, R. / Hyde, L.A. / Cox, K. / Favreau, L. / Czarniecki, M.F. / Greenlee, W.J. / McKittrick, B.A. / Parker, E.M. / Stamford, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4djv.cif.gz | 322.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4djv.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 4djv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/4djv ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4djv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46249.926 Da / Num. of mol.: 2 / Fragment: UNP Residues 41-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 277 K / Method: hanging drop / Details: Hanging Drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→20 Å / Num. obs: 104567 / % possible obs: 97.7 % / Rmerge(I) obs: 0.064 / Χ2: 1 / Net I/σ(I): 10.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→19.92 Å / Cor.coef. Fo:Fc: 0.9498 / Cor.coef. Fo:Fc free: 0.9363 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 91.89 Å2 / Biso mean: 25.7292 Å2 / Biso min: 12.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.196 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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