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- PDB-1oxq: Structure and Function Analysis of Peptide Antagonists of Melanom... -
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Basic information
Entry | Database: PDB / ID: 1oxq | ||||||
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Title | Structure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP) | ||||||
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![]() | APOPTOSIS/peptide / zinc binding / peptide complex / apoptosis inhibition / APOPTOSIS-peptide complex | ||||||
Function / homology | ![]() regulation of natural killer cell apoptotic process / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / negative regulation of necroptotic process / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / lens development in camera-type eye ...regulation of natural killer cell apoptotic process / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / CD40 receptor complex / negative regulation of necroptotic process / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / lens development in camera-type eye / intrinsic apoptotic signaling pathway in response to oxidative stress / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of tumor necrosis factor-mediated signaling pathway / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of apoptotic process / neuron apoptotic process / regulation of cell cycle / protein ubiquitination / positive regulation of apoptotic process / centrosome / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Franklin, M.C. / Kadkhodayan, S. / Ackerly, H. / Alexandru, D. / Distefano, M.D. / Elliott, L.O. / Flygare, J.A. / Vucic, D. / Deshayes, K. / Fairbrother, W.J. | ||||||
![]() | ![]() Title: Structure and Function Analysis of Peptide Antagonists of Melanoma Inhibitor of Apoptosis (ML-IAP) Authors: Franklin, M.C. / Kadkhodayan, S. / Ackerly, H. / Alexandru, D. / Distefano, M.D. / Elliott, L.O. / Flygare, J.A. / Mausisa, G. / Okawa, D.C. / Ong, D. / Vucic, D. / Deshayes, K. / Fairbrother, W.J. #1: ![]() Title: ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas Authors: Vucic, D. / Stennicke, H.R. / Pisabarro, M.T. / Salvesen, G.S. / Dixit, V.M. #2: ![]() Title: SMAC negatively regulates the anti-apoptotic activity of melanoma inhibitor of apoptosis (ML-IAP) Authors: Vucic, D. / Deshayes, K. / Ackerly, H. / Pisabarro, M.T. / Kadkhodayan, S. / Fairbrother, W.J. / Dixit, V.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 | ![]() | 127 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 705.2 KB | Display | ![]() |
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Full document | ![]() | 713.2 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oxnSC ![]() 1oy7C S: Starting model for refinement C: citing same article ( |
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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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Details | Each of the five BIR domains in the asymmetric unit represents the biologically active monomer |
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Components
#1: Protein | Mass: 15749.411 Da / Num. of mol.: 5 / Fragment: BIR domain, residues 63-179 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 943.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED / References: UniProt: Q9NR28*PLUS #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-P33 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.08 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: sodium acetate, PEG 300, DTT, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 13, 2002 |
Radiation | Monochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2686 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 64496 / Num. obs: 62709 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 41.211 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6453 / Rsym value: 0.379 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OXN Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.872 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Refinement involved replacing the peptide in 1OXN and adjusting side chains and waters. The discrepancies between observed reflections and reflections used for refinement is due to merging ...Details: Refinement involved replacing the peptide in 1OXN and adjusting side chains and waters. The discrepancies between observed reflections and reflections used for refinement is due to merging of Bijvoet mates during refinement. Since the dataset was collected at the zinc anomalous edge, the Bijvoet mates are not identical and represent crystallographically unique reflections.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.259 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. reflection obs: 59357 / % reflection Rfree: 5 % / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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