+Open data
-Basic information
Entry | Database: PDB / ID: 8dyi | ||||||
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Title | IL17A homodimer bound to Compound 5 | ||||||
Components | Interleukin-17A | ||||||
Keywords | CYTOKINE / dimer / fragment / inhibitor / antagonist | ||||||
Function / homology | Function and homology information positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / negative regulation of inflammatory response to wounding / intestinal epithelial structure maintenance / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / negative regulation of inflammatory response to wounding / intestinal epithelial structure maintenance / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Argiriadi, M.A. / Goedken, E.R. | ||||||
Funding support | 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Identification and structure-based drug design of cell-active inhibitors of interleukin 17A at a novel C-terminal site. Authors: Goedken, E.R. / Argiriadi, M.A. / Dietrich, J.D. / Petros, A.M. / Krishnan, N. / Panchal, S.C. / Qiu, W. / Wu, H. / Zhu, H. / Adams, A.M. / Bodelle, P.M. / Goguen, L. / Richardson, P.L. / ...Authors: Goedken, E.R. / Argiriadi, M.A. / Dietrich, J.D. / Petros, A.M. / Krishnan, N. / Panchal, S.C. / Qiu, W. / Wu, H. / Zhu, H. / Adams, A.M. / Bodelle, P.M. / Goguen, L. / Richardson, P.L. / Slivka, P.F. / Srikumaran, M. / Upadhyay, A.K. / Wu, B. / Judge, R.A. / Vasudevan, A. / Gopalakrishnan, S.M. / Cox, P.B. / Stoll, V.S. / Sun, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dyi.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dyi.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 8dyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dyi_validation.pdf.gz | 877.3 KB | Display | wwPDB validaton report |
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Full document | 8dyi_full_validation.pdf.gz | 881.5 KB | Display | |
Data in XML | 8dyi_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 8dyi_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/8dyi ftp://data.pdbj.org/pub/pdb/validation_reports/dy/8dyi | HTTPS FTP |
-Related structure data
Related structure data | 8dyfC 8dygC 8dyhC 4hr9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14537.343 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16552 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.67 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion / Details: 3.2M NaCl, 0.1M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→42.17 Å / Num. obs: 12501 / % possible obs: 97.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.76 Å2 / CC1/2: 0.99 / Rsym value: 0.11 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.264→2.272 Å / Num. unique obs: 102 / CC1/2: 0.802 / Rsym value: 0.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HR9 Resolution: 2.28→38.83 Å / SU ML: 0.3384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4601 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.54 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→38.83 Å
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Refine LS restraints |
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LS refinement shell |
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