+Open data
-Basic information
Entry | Database: PDB / ID: 1nme | ||||||
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Title | Structure of Casp-3 with tethered salicylate | ||||||
Components | (Caspase-3Caspase 3) x 2 | ||||||
Keywords | APOPTOSIS / HYDROLASE / cysteine proteinase / SULFONAMIDE inhibition | ||||||
Function / homology | Function and homology information caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / pyroptotic inflammatory response / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / response to amino acid / cell fate commitment / Pyroptosis / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / response to nicotine / apoptotic signaling pathway / hippocampus development / sensory perception of sound / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / protein processing / neuron differentiation / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / response to hypoxia / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Erlanson, D.A. / Lam, J. / Wiesmann, C. / Luong, T.N. / Simmons, B. / DeLano, W. / Choong, I.C. / Flanagan, M. / Lee, D. / O'Brian, T. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2003 Title: In situ assembly of enzyme inhibitors using extended tethering. Authors: Erlanson, D.A. / Lam, J.W. / Wiesmann, C. / Luong, T.N. / Simmons, R.L. / DeLano, W.L. / Choong, I.C. / Burdett, M.T. / Flanagan, W.M. / Lee, D. / Gordon, E.M. / O'Brien, T. #1: Journal: J.Med.Chem. / Year: 2002 Title: Identification of Potent and Selective Small-Molecule Inhibitors of Caspase-3 through the Use of Extended Tethering and Structure-Based Drug Design Authors: Choong, I.C. / Lew, W. / Lee, D. / Pham, P. / Burdett, M.T. / Lam, J.W. / Wiesmann, C. / Luong, T.N. / Fahr, B. / O'Brian, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nme.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nme.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nme ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nme | HTTPS FTP |
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-Related structure data
Related structure data | 1nmqC 1nmsC 1cp3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16524.814 Da / Num. of mol.: 1 / Fragment: large subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein | Mass: 10864.491 Da / Num. of mol.: 1 / Fragment: small subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
#3: Chemical | ChemComp-158 / |
#4: Chemical | ChemComp-159 / |
#5: 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: 2.19 Å3/Da / Density % sol: 43.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 37098 / Num. obs: 37098 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.043 / Net I/σ(I): 15.4 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.043 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CP3 Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.672 / SU ML: 0.057 / SU Rfree: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.819 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.633 Å / Total num. of bins used: 25 /
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |