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Open data
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Basic information
Entry | Database: PDB / ID: 1xb0 | ||||||
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Title | Structure of the BIR domain of IAP-like protein 2 | ||||||
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![]() | APOPTOSIS / SMAC / DIABLO / CASPASE INHIBITION / XIAP | ||||||
Function / homology | ![]() activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors ...activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / neuron apoptotic process / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / mitochondrion / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, H. / Renatus, M. / Eckelman, B.P. / Nunes, V.A. / Sampaio, C.A.M. / Salvesen, G.S. | ||||||
![]() | ![]() Title: The BIR domain of IAP-like protein 2 is conformationally unstable: implications for caspase inhibition Authors: Shin, H. / Renatus, M. / Eckelman, B.P. / Nunes, V.A. / Sampaio, C.A.M. / Salvesen, G.S. | ||||||
History |
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Remark 999 | SEQUENCE Residues 253-261, of chains A-F, comprise an N-terminal fusion from A-F human XIAP |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.6 KB | Display | ![]() |
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PDB format | ![]() | 112.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.6 KB | Display | ![]() |
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Full document | ![]() | 433.3 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xb1C ![]() 1g73S C: citing same article ( 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: 12349.910 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: XILP2: human ILP2 with an N-terminal fusion (residues 253-261 from human XIAP) Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 726.883 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q9NR28 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 5% PEG3000, 100mM sodium acetate, 100mM Zinc acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 44152 / % possible obs: 98.2 % / Redundancy: 5.9 % / Rsym value: 0.074 |
Reflection shell | Resolution: 2.2→2.27 Å / Rsym value: 0.382 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1G73 (chain D) Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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