+Open data
-Basic information
Entry | Database: PDB / ID: 4mti | ||||||
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Title | Crystal structure of cIAP1 BIR3 bound to T3258042 | ||||||
Components | Baculoviral IAP repeat-containing protein 2 | ||||||
Keywords | APOPTOSIS INHIBITOR / RING-type zinc finger / Ligase | ||||||
Function / homology | Function and homology information negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination ...negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / CD40 receptor complex / XY body / negative regulation of necroptotic process / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / non-canonical NF-kappaB signal transduction / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / response to cAMP / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / placenta development / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / cytoplasmic side of plasma membrane / Regulation of necroptotic cell death / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / protein-folding chaperone binding / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / regulation of cell cycle / Ub-specific processing proteases / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Snell, G.P. / Dougan, D.R. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2013 Title: Design, synthesis, and biological activities of novel hexahydropyrazino[1,2-a]indole derivatives as potent inhibitors of apoptosis (IAP) proteins antagonists with improved membrane ...Title: Design, synthesis, and biological activities of novel hexahydropyrazino[1,2-a]indole derivatives as potent inhibitors of apoptosis (IAP) proteins antagonists with improved membrane permeability across MDR1 expressing cells. Authors: Shiokawa, Z. / Hashimoto, K. / Saito, B. / Oguro, Y. / Sumi, H. / Yabuki, M. / Yoshimatsu, M. / Kosugi, Y. / Debori, Y. / Morishita, N. / Dougan, D.R. / Snell, G.P. / Yoshida, S. / Ishikawa, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mti.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mti.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 4mti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/4mti ftp://data.pdbj.org/pub/pdb/validation_reports/mt/4mti | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13294.829 Da / Num. of mol.: 2 / Fragment: Bir3 (UNP Residues 260-352) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: API1, BIRC2, IAP2, MIHB, RNF48 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BI21(DE3) References: UniProt: Q13490, 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: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 2.8M Na Cl, 0.06M Tris_base, 0.04M Tris Cl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Monochromator: single-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 14267 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Num. unique all: 669 / % possible all: 92 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.869 / SU B: 9.369 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.213 / 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: 18.769 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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