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Yorodumi- PDB-3fkt: Crystal Structure of Human Beta Secretase Complexed with Spiropip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fkt | |||||||||
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Title | Crystal Structure of Human Beta Secretase Complexed with Spiropiperdine Iminohydantoin Inhibitor | |||||||||
Components | Beta-secretase 1 | |||||||||
Keywords | HYDROLASE / ASPARTYL PROTEASE / BACE / Alternative splicing / 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 / 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: 1.9 Å | |||||||||
Authors | Munshi, S. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Discovery and X-ray Crystallographic Analysis of a Iminohydantoin Inhibitor of beta-Secretase Authors: Barrow, J.C. / Stauffer, S.R. / Rittle, K.E. / Ngo, P.L. / Yang, M.S. / Graham, S. / McGaughey, G. / Holloway, K. / Tugusheva, S.K. / Lai, M. / Espeseth, A.S. / Xu, M. / Huang, Q. / Zuck, P. ...Authors: Barrow, J.C. / Stauffer, S.R. / Rittle, K.E. / Ngo, P.L. / Yang, M.S. / Graham, S. / McGaughey, G. / Holloway, K. / Tugusheva, S.K. / Lai, M. / Espeseth, A.S. / Xu, M. / Huang, Q. / Zuck, P. / Levorse, D.A. / Hazuda, D. / Vacca, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fkt.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fkt.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fkt ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fkt | HTTPS FTP |
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-Related structure data
Related structure data | 1tqfS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45122.750 Da / Num. of mol.: 1 / Fragment: PROTEASE DOMAIN (RESIDUES 43-446) / Mutation: K95A,E97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-SII / |
#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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 7.50. Crystals were grown with L124671 and spiropiperdine iminoh was back soaked in the crystal at pH 5.0, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5413 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5413 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 40623 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.067 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.568 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TQF Resolution: 1.9→42.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.899 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / 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: 32.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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