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- PDB-5vil: Crystal structure of ASK1 kinase domain with a potent inhibitor (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vil | ||||||
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Title | Crystal structure of ASK1 kinase domain with a potent inhibitor (analog 6) | ||||||
![]() | Mitogen-activated protein kinase kinase kinase 5 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / kinase drug discovery / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of cardiac muscle cell apoptotic process / p38MAPK cascade / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / MAP kinase kinase kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of protein kinase activity / positive regulation of myoblast differentiation / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / apoptotic signaling pathway / positive regulation of JNK cascade / cellular response to hydrogen peroxide / MAPK cascade / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / Oxidative Stress Induced Senescence / neuron apoptotic process / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jasti, J. / Chang, J. / Kurumbail, R. | ||||||
![]() | ![]() Title: Rational approach to highly potent and selective apoptosis signal-regulating kinase 1 (ASK1) inhibitors. Authors: Lovering, F. / Morgan, P. / Allais, C. / Aulabaugh, A. / Brodfuehrer, J. / Chang, J. / Coe, J. / Ding, W. / Dowty, H. / Fleming, M. / Frisbie, R. / Guzova, J. / Hepworth, D. / Jasti, J. / ...Authors: Lovering, F. / Morgan, P. / Allais, C. / Aulabaugh, A. / Brodfuehrer, J. / Chang, J. / Coe, J. / Ding, W. / Dowty, H. / Fleming, M. / Frisbie, R. / Guzova, J. / Hepworth, D. / Jasti, J. / Kortum, S. / Kurumbail, R. / Mohan, S. / Papaioannou, N. / Strohbach, J.W. / Vincent, F. / Lee, K. / Zapf, C.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 462.5 KB | Display | ![]() |
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PDB format | ![]() | 386.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vioC ![]() 4bf2S 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32979.617 Da / Num. of mol.: 4 / Fragment: UNP residues 659-951 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase #2: Chemical | ChemComp-9E1 / #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.2M ammonium chloride, 0.1M Bis-Tris (pH 6.1-6.6), and 10% glycerol. PH range: 6.1-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→135 Å / Num. obs: 34591 / % possible obs: 82.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 76.18 Å2 / Rsym value: 0.031 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.64→3.73 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 9 / Num. unique obs: 19830 / Rsym value: 0.109 / % possible all: 73.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BF2 Resolution: 2.64→135 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.327 / SU Rfree Blow DPI: 0.292
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Displacement parameters | Biso mean: 122.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.64→135 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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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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