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Yorodumi- PDB-3f7g: Structure of the BIR domain from ML-IAP bound to a peptidomimetic -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f7g | ||||||
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Title | Structure of the BIR domain from ML-IAP bound to a peptidomimetic | ||||||
Components | Baculoviral IAP repeat-containing protein 7 | ||||||
Keywords | APOPTOSIS / ZINC BINDING / PEPTIDE COMPLEX / APOPTOSIS INHIBITION / PEPTIDOMIMETIC / SMALL MOLECULE / DRUG DESIGN / Metal-binding / Nucleus / Zinc-finger | ||||||
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 / difference Fourier / Resolution: 2.3 Å | ||||||
Authors | Franklin, M.C. / Fairbrother, W.J. / Cohen, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Orally bioavailable antagonists of inhibitor of apoptosis proteins based on an azabicyclooctane scaffold Authors: Cohen, F. / Alicke, B. / Elliott, L.O. / Flygare, J.A. / Goncharov, T. / Keteltas, S.F. / Franklin, M.C. / Frankovitz, S. / Stephan, J.P. / Tsui, V. / Vucic, D. / Wong, H. / Fairbrother, W.J. #1: 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. #2: 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. #3: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f7g.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f7g.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 3f7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f7g_validation.pdf.gz | 701.5 KB | Display | wwPDB validaton report |
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Full document | 3f7g_full_validation.pdf.gz | 705.6 KB | Display | |
Data in XML | 3f7g_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 3f7g_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/3f7g ftp://data.pdbj.org/pub/pdb/validation_reports/f7/3f7g | HTTPS FTP |
-Related structure data
Related structure data | 3f7hC 3f7iC 1oxnS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Unit cell |
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Details | Authors state that each asymmetric unit contains five biological units, each containing one molecule of ML-IAP with either a peptide or a peptidomimetic bound at the active site. Chains A-D form a (not biologically relevant) tetramer in which molecule A binds a peptide consisting of part of the N-terminal unstructured region of molecule D; molecule B similarly binds part of molecule C; molecule C binds molecule B; and molecule D binds molecule A. The biologically relevant complex is formed by ML-IAP molecule E binding the peptidomimetic (ligand 389). |
-Components
#1: Protein | Mass: 15765.368 Da / Num. of mol.: 5 / Fragment: BIR domain, residues 63-179 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: also known as KIAP OR MLIAP OR LIVIN, BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344 Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96CA5 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-P33 / | #4: Chemical | ChemComp-389 / | #5: 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: 2.44 Å3/Da / Density % sol: 49.64 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 2002 |
Radiation | Monochromator: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 33128 / Num. obs: 32773 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3304 / Rsym value: 0.431 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: difference Fourier Starting model: PDB entry 1OXN Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.463 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.182 / 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: 33.954 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 TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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