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Yorodumi- PDB-3eyl: Crystal structure of XIAP BIR3 domain in complex with a Smac-mime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eyl | ||||||
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Title | Crystal structure of XIAP BIR3 domain in complex with a Smac-mimetic compound | ||||||
Components | Baculoviral IAP repeat-containing protein 4 | ||||||
Keywords | LIGASE / Apoptosis / Smac-mimetics / Zinc-finger / Metal-binding / Phosphoprotein / Protease inhibitor / Thiol protease inhibitor / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Cossu, F. / Milani, M. / Mastrangelo, E. / Bolognesi, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Designing Smac-mimetics as antagonists of XIAP, cIAP1, and cIAP2. Authors: Cossu, F. / Mastrangelo, E. / Milani, M. / Sorrentino, G. / Lecis, D. / Delia, D. / Manzoni, L. / Seneci, P. / Scolastico, C. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eyl.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyl.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 3eyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyl ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyl | HTTPS FTP |
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-Related structure data
Related structure data | 3clxS S: Starting model for refinement |
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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: 14122.637 Da / Num. of mol.: 2 / Fragment: UNP residues 241-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4, API3, IAP3, XIAP / Production host: Escherichia coli (E. coli) References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: Mg formate, pH 5.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.013 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2008 |
Radiation | Monochromator: Channel-cut double-crystal silicon [111] crystal (5.2-20 keV) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.013 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 8740 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 12 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1253 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3clx Resolution: 3→38.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 32.623 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.645 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.602 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→38.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.079 Å / Rfactor Rfree error: 0.238 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 36.051 Å / Origin y: -15.941 Å / Origin z: -10.694 Å
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Refinement TLS group |
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