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Open data
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Basic information
Entry | Database: PDB / ID: 4j44 | ||||||
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Title | Crystal structure of XIAP-BIR2 domain with AIAV bound | ||||||
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![]() | APOPTOSIS / IAP / XIAP / CASPASE / SMAC / APOPTOSIS INHIBITOR | ||||||
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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lukacs, C.M. / Janson, C.A. | ||||||
![]() | ![]() Title: The structure of XIAP BIR2: understanding the selectivity of the BIR domains. Authors: Lukacs, C. / Belunis, C. / Crowther, R. / Danho, W. / Gao, L. / Goggin, B. / Janson, C.A. / Li, S. / Remiszewski, S. / Schutt, A. / Thakur, M.K. / Singh, S.K. / Swaminathan, S. / Pandey, R. ...Authors: Lukacs, C. / Belunis, C. / Crowther, R. / Danho, W. / Gao, L. / Goggin, B. / Janson, C.A. / Li, S. / Remiszewski, S. / Schutt, A. / Thakur, M.K. / Singh, S.K. / Swaminathan, S. / Pandey, R. / Tyagi, R. / Gosu, R. / Kamath, A.V. / Kuglstatter, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.2 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 444.1 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j3ySC ![]() 4j45C ![]() 4j46C ![]() 4j47C ![]() 4j48C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 9936.131 Da / Num. of mol.: 2 / Fragment: XIAP-BIR2 RESIDUES 152-236 / Mutation: C202A, C213G 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: Protein/peptide | | Mass: 372.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.84 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.7-1.9 M ammonium sulfate, 125 mM bis-tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.3→38 Å / Num. obs: 38399 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 4J3Y Resolution: 1.3→37.98 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.22 / SU ML: 0.032 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / 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: 21.006 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→37.98 Å
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Refine LS restraints |
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