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- PDB-2f3e: Crystal Structure of the Bace complex with AXQ093, a macrocyclic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f3e | ||||||
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Title | Crystal Structure of the Bace complex with AXQ093, a macrocyclic inhibitor | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE / BETA-SECRETASE / MEMAPSIN2 / ALZHEIMER'S DISEASE / ASPARTIC PROTEASE / MACROCYCLIC PEPTIDOMIMETIC INHIBITOR | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rondeau, J.-M. | ||||||
![]() | ![]() Title: Structure-based design and synthesis of macroheterocyclic peptidomimetic inhibitors of the aspartic protease beta-site amyloid precursor protein cleaving enzyme (BACE). Authors: Hanessian, S. / Yang, G. / Rondeau, J.-M. / Neumann, U. / Betschart, C. / Tintelnot-Blomley, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.4 KB | Display | ![]() |
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PDB format | ![]() | 200.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS A MONOMER |
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Components
#1: Protein | Mass: 44777.336 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.62 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.0M ammonium phosphate, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 3, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. all: 93683 / Num. obs: 93683 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.102 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.405 / Num. unique all: 9341 / Χ2: 0.858 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.352 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.11→63.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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