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Yorodumi- PDB-2ph8: Crystal Structure of Human Beta Secretase Complexed with inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ph8 | ||||||
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Title | Crystal Structure of Human Beta Secretase Complexed with inhibitor | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / ASPARTYL PROTEASE / BACE | ||||||
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 / detection of mechanical stimulus involved in sensory perception of pain / cellular response to manganese ion / 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 / detection of mechanical stimulus involved in sensory perception of pain / cellular response to manganese ion / amyloid-beta metabolic process / 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 / recycling endosome / protein processing / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / early endosome / aspartic-type endopeptidase activity / 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: 1.7 Å | ||||||
Authors | Munshi, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Strategies toward improving the brain penetration of macrocyclic tertiary carbinamine BACE-1 inhibitors. Authors: Moore, K.P. / Zhu, H. / Rajapakse, H.A. / McGaughey, G.B. / Colussi, D. / Price, E.A. / Sankaranarayanan, S. / Simon, A.J. / Pudvah, N.T. / Hochman, J.H. / Allison, T. / Munshi, S.K. / ...Authors: Moore, K.P. / Zhu, H. / Rajapakse, H.A. / McGaughey, G.B. / Colussi, D. / Price, E.A. / Sankaranarayanan, S. / Simon, A.J. / Pudvah, N.T. / Hochman, J.H. / Allison, T. / Munshi, S.K. / Graham, S.L. / Vacca, J.P. / Nantermet, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ph8.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ph8.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ph8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ph8_validation.pdf.gz | 472.2 KB | Display | wwPDB validaton report |
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Full document | 2ph8_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 2ph8_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2ph8_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2ph8 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2ph8 | HTTPS FTP |
-Related structure data
Related structure data | 2qzkC 1tqfS S: Starting model for refinement 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 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: K75A, E77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 | ||||
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#2: Chemical | #3: Chemical | ChemComp-35A / | #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: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystals were grown with L124671 and inhibitor was back soaked in the crystal at pH 5.0. 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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 / Date: Mar 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5413 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 56340 / % possible obs: 100 % / Redundancy: 6.2 % / Rsym value: 0.046 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.49 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1TQF Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.659 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.086 / 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: 27.379 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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