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Open data
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Basic information
Entry | Database: PDB / ID: 1xb1 | ||||||
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Title | The Structure of the BIR domain of IAP-like protein 2 | ||||||
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![]() | APOPTOSIS / IAP / caspase inhibition / SMAC / Diabolo | ||||||
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 | ![]() | 134.2 KB | Display | ![]() |
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PDB format | ![]() | 110.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.6 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 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: 2.77 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 5% PEG3000, 100mM Na 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 22931 / % possible obs: 92.9 % / Redundancy: 3 % / Rsym value: 0.071 |
Reflection shell | Resolution: 2.7→2.8 Å / Rsym value: 0.374 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.4149 Å2 / ksol: 0.363543 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 44.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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