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Yorodumi- PDB-5nx1: Combinatorial Engineering of Proteolytically Resistant APPI Varia... -
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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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Keywords | HYDROLASE / Serine_protease / inhibitor / complex | ||||||
| Function / homology | Function and homology informationcornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / amyloid precursor protein metabolic process ...cornified envelope / tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / amyloid precursor protein metabolic process / hormone metabolic process / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Lysosome Vesicle Biogenesis / astrocyte projection / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / regulation of neuron projection development / dendrite development / positive regulation of protein metabolic process / TRAF6 mediated NF-kB activation / protein autoprocessing / regulation of cell differentiation / collagen catabolic process / Advanced glycosylation endproduct receptor signaling / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / The NLRP3 inflammasome / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / transition metal ion binding / main axon / intracellular copper ion homeostasis / regulation of multicellular organism growth / ECM proteoglycans / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / Purinergic signaling in leishmaniasis infection / intercellular bridge / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / myelination / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / response to interleukin-1 / protein serine/threonine kinase binding / cellular response to copper ion / secretory granule / platelet alpha granule lumen / cellular response to cAMP / protein maturation / positive regulation of glycolytic process / central nervous system development / endosome lumen / positive regulation of interleukin-1 beta production / dendritic shaft / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / adult locomotory behavior / learning / positive regulation of JNK cascade / Post-translational protein phosphorylation / locomotory behavior / serine-type endopeptidase inhibitor activity / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / regulation of long-term neuronal synaptic plasticity / cellular response to nerve growth factor stimulus / synapse organization / recycling endosome / visual learning / response to lead ion / response to wounding / positive regulation of interleukin-6 production / Golgi lumen / cognition Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å | ||||||
Authors | Shahar, A. / Sananes, A. / Radisky, E.S. / Papo, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2018Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5nx1.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5nx1.ent.gz | 119.1 KB | Display | PDB format |
| PDBx/mmJSON format | 5nx1.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5nx1_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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| Full document | 5nx1_full_validation.pdf.gz | 450 KB | Display | |
| Data in XML | 5nx1_validation.xml.gz | 15.7 KB | Display | |
| Data in CIF | 5nx1_validation.cif.gz | 22.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/5nx1 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nx1 | 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.) Homo sapiens (human) / Gene: KLK6, PRSS18, PRSS9 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)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.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067 |
| #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.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067 |
| #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.) Homo sapiens (human) / Gene: APP, A4, AD1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P05067 |
| #5: Water | ChemComp-HOH / |
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.969 Å |
| 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: MOLECULAR REPLACEMENTStarting 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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| 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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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
Citation










PDBj















Trichoplusia ni (cabbage looper)
Komagataella phaffii GS115 (fungus)
