+Open data
-Basic information
Entry | Database: PDB / ID: 3ine | ||||||
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Title | Bace1 with the aminohydantoin Compound S-34 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / Bace1 / xray / inhibitor / Alternative splicing / Aspartyl protease / Disulfide bond / Glycoprotein / Membrane / Polymorphism / Protease / Transmembrane / Zymogen | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.996 Å | ||||||
Authors | Olland, A.M. / Chopra, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Design and synthesis of 5,5'-disubstituted aminohydantoins as potent and selective human beta-secretase (BACE1) inhibitors. Authors: Malamas, M.S. / Erdei, J. / Gunawan, I. / Turner, J. / Hu, Y. / Wagner, E. / Fan, K. / Chopra, R. / Olland, A. / Bard, J. / Jacobsen, S. / Magolda, R.L. / Pangalos, M. / Robichaud, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ine.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ine.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ine.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ine_validation.pdf.gz | 451.5 KB | Display | wwPDB validaton report |
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Full document | 3ine_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 3ine_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3ine_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3ine ftp://data.pdbj.org/pub/pdb/validation_reports/in/3ine | HTTPS FTP |
-Related structure data
Related structure data | 3indC 3infC 3inhC 1w50S C: citing same article (ref.) S: Starting model for refinement |
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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: 46440.980 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-X17 / ( |
#3: 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: 2.03 Å3/Da / Density % sol: 39.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 8% PEG 3350, 100 mM NaAcetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Date: Nov 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.996 Å / Num. obs: 23067 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W50 Highest resolution: 1.996 Å / SU ML: 0.3 / σ(F): 1.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.594 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.996 Å
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Refine LS restraints |
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LS refinement shell |
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