[English] 日本語
Yorodumi- PDB-4wvt: Crystal structure of XIAP-BIR2 domain complexed with ligand bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wvt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of XIAP-BIR2 domain complexed with ligand bound | ||||||
Components |
| ||||||
Keywords | APOPTOSIS / IAP / XIAP-BIR2 | ||||||
Function / homology | Function and homology information endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Pokross, M.E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: The Discovery of Macrocyclic XIAP Antagonists from a DNA-Programmed Chemistry Library, and Their Optimization To Give Lead Compounds with in Vivo Antitumor Activity. Authors: Seigal, B.A. / Connors, W.H. / Fraley, A. / Borzilleri, R.M. / Carter, P.H. / Emanuel, S.L. / Fargnoli, J. / Kim, K. / Lei, M. / Naglich, J.G. / Pokross, M.E. / Posy, S.L. / Shen, H. / ...Authors: Seigal, B.A. / Connors, W.H. / Fraley, A. / Borzilleri, R.M. / Carter, P.H. / Emanuel, S.L. / Fargnoli, J. / Kim, K. / Lei, M. / Naglich, J.G. / Pokross, M.E. / Posy, S.L. / Shen, H. / Surti, N. / Talbott, R. / Zhang, Y. / Terrett, N.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wvt.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wvt.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/4wvt ftp://data.pdbj.org/pub/pdb/validation_reports/wv/4wvt | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11359.649 Da / Num. of mol.: 2 / Mutation: C202A, C231G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.67 Å3/Da / Density % sol: 28.73 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: .98 M Ammonium Sulfate and .1M Ammonium Formate. Single crystals formed after streak seeding. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 3, 2010 |
Radiation | Monochromator: MicoMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 10044 / % possible obs: 97.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 21.09 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.96→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.7 / Rsym value: 0 / % possible all: 75.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→25.15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.8956 / SU R Cruickshank DPI: 0.236 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.181
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.75 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.209 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→25.15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.96→2.19 Å / Total num. of bins used: 5
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|