+Open data
-Basic information
Entry | Database: PDB / ID: 6y8i | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Fragment KCL_I013 in complex with IL-1-beta | |||||||||
Components | Interleukin-1 betaInterleukin 1 beta | |||||||||
Keywords | SIGNALING PROTEIN / FBDD / FRAGMENT BASED DRUG DESIGN / XCHEM / IL1B | |||||||||
Function / homology | Function and homology information smooth muscle adaptation / positive regulation of T cell mediated immunity / hyaluronan biosynthetic process / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production ...smooth muscle adaptation / positive regulation of T cell mediated immunity / hyaluronan biosynthetic process / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of glucose transmembrane transport / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / cellular response to interleukin-17 / sequestering of triglyceride / positive regulation of RNA biosynthetic process / monocyte aggregation / positive regulation of prostaglandin secretion / negative regulation of gap junction assembly / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / fever generation / regulation of defense response to virus by host / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / positive regulation of membrane protein ectodomain proteolysis / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of monocyte chemotactic protein-1 production / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / negative regulation of synaptic transmission / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / positive regulation of heterotypic cell-cell adhesion / positive regulation of p38MAPK cascade / cellular response to organic substance / regulation of nitric-oxide synthase activity / response to ATP / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell division / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of neurogenesis / positive regulation of vascular endothelial growth factor production / positive regulation of epithelial to mesenchymal transition / ectopic germ cell programmed cell death / Pyroptosis / Purinergic signaling in leishmaniasis infection / negative regulation of lipid catabolic process / JNK cascade / positive regulation of glial cell proliferation / negative regulation of insulin receptor signaling pathway / embryo implantation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / response to interleukin-1 / regulation of ERK1 and ERK2 cascade / neutrophil chemotaxis / negative regulation of MAP kinase activity / positive regulation of mitotic nuclear division / positive regulation of interleukin-2 production / positive regulation of protein export from nucleus / canonical NF-kappaB signal transduction / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of MAP kinase activity / positive regulation of inflammatory response / Interleukin-1 signaling / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of neurogenesis / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / cellular response to xenobiotic stimulus / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / immune response / inflammatory response / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of cell population proliferation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | |||||||||
Authors | De Nicola, G.F. / Nichols, C.E. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: To Be Published Title: Fragment KCL_I013 in complex with IL-1-beta Authors: De Nicola, G.F. / Nichols, C.E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6y8i.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6y8i.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 6y8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y8i ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y8i | HTTPS FTP |
---|
-Related structure data
Related structure data | 5r85S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17395.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01584 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-OGE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.27 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.8M ammonium sulphate and 0.1M Tris pH7.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→37.79 Å / Num. obs: 37604 / % possible obs: 97 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.27 Å2 / CC1/2: 1 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.46→1.49 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1878 / CC1/2: 0.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5R85 Resolution: 1.46→24.5 Å / SU ML: 0.2014 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.7472
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→24.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|