+Open data
-Basic information
Entry | Database: PDB / ID: 1nms | ||||||
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Title | Caspase-3 tethered to irreversible inhibitor | ||||||
Components | Caspase-3 | ||||||
Keywords | APOPTOSIS / HYDROLASE / Caspase-3 / tether / irreversible / inhibitor | ||||||
Function / homology | Function and homology information caspase-3 / anterior neural tube closure / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / 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 / response to cobalt ion ...caspase-3 / anterior neural tube closure / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / 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 / response to cobalt ion / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cellular response to staurosporine / cyclin-dependent protein serine/threonine kinase inhibitor activity / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Apoptotic cleavage of cell adhesion proteins / 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 / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / execution phase of apoptosis / 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 / response to amino acid / cell fate commitment / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / Pyroptosis / response to tumor necrosis factor / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / regulation of protein stability / response to hydrogen peroxide / protein catabolic process / protein processing / neuron differentiation / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Erlanson, D.A. / Lam, J. / Wiesmann, C. / Luong, T.N. / Simmons, R.L. / DeLano, W.L. / Choong, I.C. / Flanagan, W.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 | 1nms.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nms.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nms_validation.pdf.gz | 972.6 KB | Display | wwPDB validaton report |
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Full document | 1nms_full_validation.pdf.gz | 980.5 KB | Display | |
Data in XML | 1nms_validation.xml.gz | 27 KB | Display | |
Data in CIF | 1nms_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nms ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nms | HTTPS FTP |
-Related structure data
Related structure data | 1nmeC 1nmqC 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: 28518.500 Da / Num. of mol.: 2 / 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.7 % | ||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 62041 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Rsym value: 0.053 / Net I/σ(I): 12.2 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / % possible obs: 98.8 % / Rmerge(I) obs: 0.053 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CP3 Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.586 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.735 Å / Total num. of bins used: 25 /
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.183 / Rfactor Rwork: 0.151 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |