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- PDB-2fqq: Crystal structure of human caspase-1 (Cys285->Ala, Cys362->Ala, C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fqq | ||||||
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Title | Crystal structure of human caspase-1 (Cys285->Ala, Cys362->Ala, Cys364->Ala, Cys397->Ala) in complex with 1-methyl-3-trifluoromethyl-1H-thieno[2,3-c]pyrazole-5-carboxylic acid (2-mercapto-ethyl)-amide | ||||||
![]() | (Caspase-1) x 2 | ||||||
![]() | HYDROLASE / Caspase / allosteric inhibitor | ||||||
Function / homology | ![]() caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / The IPAF inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / osmosensory signaling pathway / Interleukin-37 signaling / pattern recognition receptor signaling pathway / : / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / 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 / microtubule / defense response to virus / endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / nucleolus / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Scheer, J.M. / Wells, J.A. / Romanowski, M.J. | ||||||
![]() | ![]() Title: A common allosteric site and mechanism in caspases Authors: Scheer, J.M. / Romanowski, M.J. / Wells, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.7 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 686.7 KB | Display | ![]() |
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Full document | ![]() | 687.5 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2h48C ![]() 2hbqC ![]() 2hbrC ![]() 2hbyC ![]() 2hbzC ![]() 1sc1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | Heterotetramer (dimer of two heterodimers). Each heterodimer is represented by chains A (the p20 subunit) and B (the p10 subunit) of human caspase-1. |
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Components
#1: Protein | Mass: 19837.773 Da / Num. of mol.: 1 / Fragment: p20 subunit, residues 120-297 / Mutation: C285A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10162.559 Da / Num. of mol.: 1 / Fragment: p10 subunit, residues 317-404 / Mutation: C362A, C364A, C397A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-F1G / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10 mM HEPES, 16.5% PEG 3350, 250 mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 2004 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. all: 11608 / Num. obs: 5490 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 5 |
Reflection shell | Resolution: 3.3→3.48 Å / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SC1 Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.817 / SU B: 62.137 / SU ML: 0.464 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.567 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.207 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.413 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: 41.0054 Å / Origin y: 28.1484 Å / Origin z: 34.1417 Å
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