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Yorodumi- PDB-4rce: Crystal structure of BACE1 in complex with aminooxazoline xanthen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rce | ||||||
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Title | Crystal structure of BACE1 in complex with aminooxazoline xanthene inhibitor 2 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / aspartic protease / Alzheimer's disease / APP / amyloid precursor protein / brain / 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 / amyloid-beta metabolic process / prepulse inhibition ...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 / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Whittington, D.A. / Long, A.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Lead Optimization and Modulation of hERG Activity in a Series of Aminooxazoline Xanthene beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1) Inhibitors. Authors: Epstein, O. / Bryan, M.C. / Cheng, A.C. / Derakhchan, K. / Dineen, T.A. / Hickman, D. / Hua, Z. / Human, J.B. / Kreiman, C. / Marx, I.E. / Weiss, M.M. / Wahl, R.C. / Wen, P.H. / Whittington, ...Authors: Epstein, O. / Bryan, M.C. / Cheng, A.C. / Derakhchan, K. / Dineen, T.A. / Hickman, D. / Hua, Z. / Human, J.B. / Kreiman, C. / Marx, I.E. / Weiss, M.M. / Wahl, R.C. / Wen, P.H. / Whittington, D.A. / Wood, S. / Zheng, X.M. / Fremeau, R.T. / White, R.D. / Patel, V.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rce.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rce.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/4rce ftp://data.pdbj.org/pub/pdb/validation_reports/rc/4rce | 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: 45822.445 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 43-453) / Mutation: R(-5)K, R(-4)K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2 | ||
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#2: Chemical | ChemComp-3LN / ( | ||
#3: Chemical | #4: 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: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.6 Details: 20% polyethylene glycol 5000 monomethyl ether, 200 mM ammonium iodide, 180 mM sodium citrate, pH 6.6, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 98 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 2, 2008 / Details: Varimax HR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. all: 21318 / Num. obs: 21126 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.213 / Χ2: 1.077 / Net I/σ(I): 10.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2172 / WRfactor Rwork: 0.1723 / FOM work R set: 0.8472 / SU B: 6.786 / SU ML: 0.159 / SU R Cruickshank DPI: 0.3142 / SU Rfree: 0.2395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 116.94 Å2 / Biso mean: 28.506 Å2 / Biso min: 11.17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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