+Open data
-Basic information
Entry | Database: PDB / ID: 6qci | ||||||
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Title | Structure of XIAP-BIR1 V86E mutant | ||||||
Components | E3 ubiquitin-protein ligase XIAP | ||||||
Keywords | APOPTOSIS / BIR / NF-KB / XIAP / CANCER / DOCKING / INHIBITOR | ||||||
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 / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response ...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 / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / protein serine/threonine kinase binding / Regulation of PTEN localization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of canonical Wnt signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of inflammatory response / regulation of cell population proliferation / positive regulation of canonical NF-kappaB signal transduction / neuron apoptotic process / regulation of apoptotic process / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sorrentino, L. / Cossu, F. / Milani, M. / Mastrangelo, E. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Chemistryopen / Year: 2019 Title: Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1. Authors: Sorrentino, L. / Cossu, F. / Milani, M. / Malkoc, B. / Huang, W.C. / Tsay, S.C. / Ru Hwu, J. / Mastrangelo, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qci.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qci.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qci_validation.pdf.gz | 479.2 KB | Display | wwPDB validaton report |
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Full document | 6qci_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 6qci_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6qci_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/6qci ftp://data.pdbj.org/pub/pdb/validation_reports/qc/6qci | HTTPS FTP |
-Related structure data
Related structure data | 6gjwC 4oxcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 12387.718 Da / Num. of mol.: 4 / Mutation: V86E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG References: UniProt: P98170, RING-type E3 ubiquitin transferase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-PEG / | #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: 1.87 Å3/Da / Density % sol: 34.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris, pH 8.0, 0.2 M lithium sulphate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2017 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→36.35 Å / Num. obs: 16267 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 4.4 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.36 Å |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OXC Resolution: 2.3→36.35 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.849 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.06 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.301 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→36.35 Å
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