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Yorodumi- PDB-2i3h: Structure of an ML-IAP/XIAP chimera bound to a 4-mer peptide (AVPW) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i3h | ||||||
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Title | Structure of an ML-IAP/XIAP chimera bound to a 4-mer peptide (AVPW) | ||||||
Components |
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Keywords | INHIBITOR/APOPTOSIS / ZINC BINDING / PEPTIDE COMPLEX / APOPTOSIS INHIBITION / PEPTIDOMIMETIC / SMALL MOLECULE / DRUG DESIGN / INHIBITOR-APOPTOSIS COMPLEX | ||||||
Function / homology | Function and homology information regulation of natural killer cell apoptotic process / negative regulation of necroptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...regulation of natural killer cell apoptotic process / negative regulation of necroptotic process / lens development in camera-type eye / cysteine-type endopeptidase inhibitor activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of protein ubiquitination / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of apoptotic process / regulation of cell cycle / protein ubiquitination / centrosome / apoptotic process / negative regulation of apoptotic process / Golgi apparatus / enzyme binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.62 Å | ||||||
Authors | Fairbrother, W.J. / Franklin, M.C. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2006 Title: Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs. Authors: Zobel, K. / Wang, L. / Varfolomeev, E. / Franklin, M.C. / Elliott, L.O. / Wallweber, H.J. / Okawa, D.C. / Flygare, J.A. / Vucic, D. / Fairbrother, W.J. / Deshayes, K. #1: Journal: Biochem.J. / Year: 2005 Title: Engineering ML-IAP to produce an extraordinarily potent caspase-9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP Authors: Vucic, D. / Franklin, M.C. / Wallweber, H.J. / Das, K. / Eckelman, B.P. / Shin, H. / Elliott, L.O. / Deshayes, K. / Salvesen, G.S. / Fairbrother, W.J. #2: Journal: Biochemistry / Year: 2003 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. / Vucic, D. / Deshayes, K. / Fairbrother, W.J. | ||||||
History |
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Remark 999 | SEQUENCE For entity 1 (chains A and B) residues 150, 160-168, and 172 replaced with XIAP-BIR3 homologues. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i3h.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i3h.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 2i3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i3h_validation.pdf.gz | 481.7 KB | Display | wwPDB validaton report |
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Full document | 2i3h_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 2i3h_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 2i3h_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/2i3h ftp://data.pdbj.org/pub/pdb/validation_reports/i3/2i3h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 14977.567 Da / Num. of mol.: 2 / Fragment: ML-IAP residues 63-172 Mutation: RESIDUES 150, 160-168, AND 172 REPLACED WITH XIAP-BIR3 HOMOLOGUES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC7 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96CA5 #2: Protein/peptide | Mass: 471.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized peptide |
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-Non-polymers , 5 types, 239 molecules
#3: Chemical | #4: Chemical | ChemComp-LI / | #5: Chemical | ChemComp-BTB / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Lithium sulfate, PEG 3350, Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: SBC / Detector: CCD / Date: Aug 15, 2003 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. all: 37115 / Num. obs: 32349 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 0.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1397 / % possible all: 38.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1.3 A structure of the ML-IAP/XIAP protein bound to a different peptidomimetic, with the ligand and surrounding waters removed Resolution: 1.62→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.519 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.075 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.726 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.662 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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