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- PDB-3g76: Crystal structure of XIAP-BIR3 in complex with a bivalent compound -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g76 | ||||||
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Title | Crystal structure of XIAP-BIR3 in complex with a bivalent compound | ||||||
![]() | Baculoviral IAP repeat-containing protein 4 | ||||||
![]() | LIGASE / Apoptosis / IAP / SmacDIABLO / peptidomimetics / pro-apoptotic drugs / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Protease inhibitor / Thiol protease inhibitor / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger | ||||||
Function / homology | ![]() 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 / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / 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 / 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 / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cossu, F. / Milani, M. / Mastrangelo, E. / Bolognesi, M. | ||||||
![]() | ![]() Title: Structural basis for bivalent smac-mimetics recognition in the IAP protein family Authors: Cossu, F. / Milani, M. / Mastrangelo, E. / Vachette, P. / Servida, F. / Lecis, D. / Canevari, G. / Delia, D. / Drago, C. / Rizzo, V. / Manzoni, L. / Seneci, P. / Scolastico, C. / Bolognesi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 377.4 KB | Display | ![]() |
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PDB format | ![]() | 311.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | 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 |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14122.637 Da / Num. of mol.: 8 / Fragment: BIR3 domain, UNP residues 241-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CZ3 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 20% PEG MME 2000, 60mM sodium acetate tri-hydrate, 120mM Ammonium sulfate, 400mM sodium-potassium tartrate tetra-hydrate, pH 4.6, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007 Details: Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror |
Radiation | Monochromator: high resolution Si(311) cut and a lower resolution Si(111) cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 33440 / Redundancy: 3.6 % / Rmerge(I) obs: 0.101 |
Reflection shell | Highest resolution: 3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4861 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BIR3 DOMAIN FROM PDB ENTRY 3CLX Resolution: 3→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.819 / Occupancy max: 1 / Occupancy min: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.613 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.64 Å2 / Biso mean: 72.888 Å2 / Biso min: 4.37 Å2
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 29.741 Å / Origin y: 17.166 Å / Origin z: 24.886 Å
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Refinement TLS group |
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