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- PDB-5nx1: Combinatorial Engineering of Proteolytically Resistant APPI Varia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nx1 | ||||||
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Title | Combinatorial Engineering of Proteolytically Resistant APPI Variants that Selectively Inhibit Human Kallikrein 6 for Cancer Therapy | ||||||
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![]() | HYDROLASE / Serine_protease / inhibitor / complex | ||||||
Function / homology | ![]() positive regulation of G protein-coupled receptor signaling pathway / tissue regeneration / cornified envelope / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / hormone metabolic process / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway ...positive regulation of G protein-coupled receptor signaling pathway / tissue regeneration / cornified envelope / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / hormone metabolic process / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / amyloid precursor protein metabolic process / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / regulation of neuron projection development / Golgi-associated vesicle / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / intercellular bridge / : / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / regulation of cell differentiation / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / protein autoprocessing / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / intracellular copper ion homeostasis / negative regulation of neuron differentiation / collagen catabolic process / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / myelination / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / secretory granule / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shahar, A. / Sananes, A. / Radisky, E.S. / Papo, N. | ||||||
![]() | ![]() Title: A potent, proteolysis-resistant inhibitor of kallikrein-related peptidase 6 (KLK6) for cancer therapy, developed by combinatorial engineering. Authors: Sananes, A. / Cohen, I. / Shahar, A. / Hockla, A. / De Vita, E. / Miller, A.K. / Radisky, E.S. / Papo, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.2 KB | Display | ![]() |
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PDB format | ![]() | 119.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nx3C ![]() 1aapS ![]() 1lo6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24417.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q92876, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein/peptide | Mass: 2945.086 Da / Num. of mol.: 1 / Fragment: UNP residues 289-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 6295.999 Da / Num. of mol.: 1 / Fragment: UNP residues 302-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 9223.071 Da / Num. of mol.: 1 / Fragment: UNP residues 289-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5, 25% Polyethylene Glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 1.853→47.262 Å / Num. obs: 36867 / % possible obs: 99.52 % / Redundancy: 2 % / Rpim(I) all: 0.031 / Net I/σ(I): 13.48 |
Reflection shell | Resolution: 1.853→1.92 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.08 / Num. unique all: 3528 / CC1/2: 0.574 / Rpim(I) all: 0.642 / % possible all: 96.37 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AAP & 1LO6 Resolution: 1.853→47.262 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.853→47.262 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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