+Open data
-Basic information
Entry | Database: PDB / ID: 3lnk | ||||||
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Title | Structure of BACE bound to SCH743813 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / Alzheimer's / BACE1 / Alternative splicing / Aspartyl protease / Disulfide bond / Endoplasmic reticulum / Endosome / Glycoprotein / Golgi apparatus / 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 / protein serine/threonine kinase binding / 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 / protein processing / recycling endosome / 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 / aspartic-type endopeptidase activity / lysosome / 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: 1.8 Å | ||||||
Authors | Orth, P. / Cumming, J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Piperazine sulfonamide BACE1 inhibitors: design, synthesis, and in vivo characterization. Authors: Cumming, J. / Babu, S. / Huang, Y. / Carrol, C. / Chen, X. / Favreau, L. / Greenlee, W. / Guo, T. / Kennedy, M. / Kuvelkar, R. / Le, T. / Li, G. / McHugh, N. / Orth, P. / Ozgur, L. / Parker, ...Authors: Cumming, J. / Babu, S. / Huang, Y. / Carrol, C. / Chen, X. / Favreau, L. / Greenlee, W. / Guo, T. / Kennedy, M. / Kuvelkar, R. / Le, T. / Li, G. / McHugh, N. / Orth, P. / Ozgur, L. / Parker, E. / Saionz, K. / Stamford, A. / Strickland, C. / Tadesse, D. / Voigt, J. / Zhang, L. / Zhang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lnk.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lnk.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lnk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3lnk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3lnk_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 3lnk_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3lnk ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3lnk | HTTPS FTP |
-Related structure data
Related structure data | 3lpiC 3lpjC 3lpkC 2qp8S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44023.629 Da / Num. of mol.: 2 / Fragment: UNP residues 53 to 447 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.32 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 19, 2009 / Details: Osmic |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 94997 / Num. obs: 94237 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.84 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 10 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QP8 Resolution: 1.8→26.48 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.192 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→26.48 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.8 Å / Total num. of bins used: 20
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