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Yorodumi- PDB-3cm2: Crystal Structure of XIAP BIR3 domain in complex with a Smac-mime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cm2 | ||||||
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Title | Crystal Structure of XIAP BIR3 domain in complex with a Smac-mimetic compound, Smac010 | ||||||
Components | Baculoviral IAP repeat-containing protein 4 | ||||||
Keywords | Ligase / Apoptosis / Zinc-finger / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Protease inhibitor / Thiol protease inhibitor / Ubl conjugation / 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 / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response ...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 / 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 / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / protein serine/threonine kinase binding / 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 / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / regulation of inflammatory response / regulation of apoptotic process / neuron 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 / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Cossu, F. / Mastrangelo, E. / Milani, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Targeting the X-linked inhibitor of apoptosis protein through 4-substituted azabicyclo[5.3.0]alkane smac mimetics. Structure, activity, and recognition principles. Authors: Mastrangelo, E. / Cossu, F. / Milani, M. / Sorrentino, G. / Lecis, D. / Delia, D. / Manzoni, L. / Drago, C. / Seneci, P. / Scolastico, C. / Rizzo, V. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cm2.cif.gz | 234.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cm2.ent.gz | 190.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cm2_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 3cm2_full_validation.pdf.gz | 3.7 MB | Display | |
Data in XML | 3cm2_validation.xml.gz | 47.6 KB | Display | |
Data in CIF | 3cm2_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/3cm2 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/3cm2 | HTTPS FTP |
-Related structure data
Related structure data | 3clxSC 3cm7C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 14675.340 Da / Num. of mol.: 10 / 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 | ChemComp-ZN / #3: Chemical | ChemComp-X23 / ( #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: 3.22 Å3/Da / Density % sol: 61.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 12% PEG 10K, 10% glycerol, 0.1M NaCl, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 66532 / Num. obs: 66464 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 14 |
Reflection shell | Highest resolution: 2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CLX Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.322 / ESU R Free: 0.253 / 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: 51.255 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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