+Open data
-Basic information
Entry | Database: PDB / ID: 2qzk | ||||||
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Title | Crystal structure of human Beta Secretase complexed with I21 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / ASPARTYL PROTEASE / BACE / Alternative splicing / Glycoprotein / Membrane / 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 / 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 / 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: 1.8 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 | 2qzk.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qzk.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/2qzk ftp://data.pdbj.org/pub/pdb/validation_reports/qz/2qzk | HTTPS FTP |
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-Related structure data
Related structure data | 2ph8C 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
#1: Protein | Mass: 45122.750 Da / Num. of mol.: 1 / Fragment: UNP residues 43-446 / Mutation: K136A, E138A 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 | ChemComp-I21 / |
#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: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, Crystals were grown with L124671 and inh 416198 was back soaked, 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: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 47211 / Num. obs: 45268 / % possible obs: 95.9 % / Redundancy: 3.88 % / Rsym value: 0.098 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 4703 / Rsym value: 0.525 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TQF Resolution: 1.8→20 Å
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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