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- PDB-2zjm: Crystal structure of the human BACE1 catalytic domain in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zjm | ||||||
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Title | Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-chloro-2-isopropoxy-3-methoxy-benzyl)-piperidin-4-yl]-2-(4-sulfamoyl-phenoxy)-acetamide | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE / BACE / small-molecule inhibitor / fragment-based discovery / Alternative splicing / Aspartyl protease / Glycoprotein / Membrane / Protease / Transmembrane / Zymogen | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Allison, T.J. / Pham, P. / Romanowski, M.J. / Munshi, S.K. | ||||||
![]() | ![]() Title: Fragment-based discovery of novel BACE1 inhibitors using Tethering technology Authors: Yang, W. / Fucini, R.V. / Fahr, B.T. / Randal, M. / Lind, K.E. / Lam, M.B. / Lu, W. / Lu, Y. / Cary, D.R. / Romanowski, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.8 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 753.3 KB | Display | ![]() |
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Full document | ![]() | 761.9 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zjhC ![]() 2zjiC ![]() 2zjjC ![]() 2zjkC ![]() 2zjlC ![]() 2zjnC ![]() 2p8hS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: K75A, E77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-F1M / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M HEPES (pH 7.5), 1.5M Li2SO4, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 11, 2004 / Details: VARIMAX-HF OPTIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 40419 / % possible obs: 100 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.454 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2P8H Resolution: 1.9→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 455927.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: BABINET / Bsol: 280 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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