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Yorodumi- PDB-1rwx: Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rwx | ||||||
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Title | Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-yloxy)-benzoylamino]-2-thiophen-2-yl-hexanoylamino}-butyric acid | ||||||
Components | (Interleukin-1 beta convertase) x 2 | ||||||
Keywords | HYDROLASE / protein-small molecule inhibitor complex | ||||||
Function / homology | Function and homology information caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / caspase binding / CARD domain binding / osmosensory signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / cytokine binding / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / The NLRP3 inflammasome / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / cellular response to type II interferon / kinase binding / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / endopeptidase activity / microtubule / defense response to bacterium / cysteine-type endopeptidase activity / nucleolus / apoptotic process / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Romanowski, M.J. / Fahr, B.T. / O'Brien, T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Tethering identifies fragment that yields potent inhibitors of human caspase-1. Authors: Fahr, B.T. / O'Brien, T. / Pham, P. / Waal, N.D. / Baskaran, S. / Raimundo, B.C. / Lam, J.W. / Sopko, M.M. / Purkey, H.E. / Romanowski, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rwx.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rwx.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwx ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwx | HTTPS FTP |
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-Related structure data
Related structure data | 1rwwC 1rwnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19869.838 Da / Num. of mol.: 1 / Fragment: INTERLEUKIN-1 BETA CONVERTASE P20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P29466, caspase-1 |
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#2: Protein | Mass: 10258.755 Da / Num. of mol.: 1 / Fragment: INTERLEUKIN-1 BETA CONVERTASE P10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P29466, caspase-1 |
#3: Chemical | ChemComp-YBH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M PIPES, 88mM (NH4)2SO4, 25% PEG 2000 MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2003 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 29162 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.85→1.91 Å / Rmerge(I) obs: 0.38 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1RWN Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.277 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.925 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.914 Å / Total num. of bins used: 15 /
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