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Yorodumi- PDB-1nbp: Crystal Structure Of Human Interleukin-2 Y31C Covalently Modified... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nbp | ||||||
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Title | Crystal Structure Of Human Interleukin-2 Y31C Covalently Modified At C31 With 3-Mercapto-1-(1,3,4,9-tetrahydro-B-carbolin-2-yl)-propan-1-one | ||||||
Components | Interleukin-2 | ||||||
Keywords | CYTOKINE / FOUR-HELIX BUNDLE / SMALL MOLECULE COMPLEX | ||||||
Function / homology | Function and homology information kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / kinase activator activity / positive regulation of regulatory T cell differentiation / : / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of protein phosphorylation / cytokine activity / negative regulation of inflammatory response / growth factor activity / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / RAF/MAP kinase cascade / positive regulation of cell growth / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hyde, J. / Braisted, A.C. / Randal, M. / Arkin, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Discovery and characterization of cooperative ligand binding in the adaptive region of interleukin-2 Authors: Hyde, J. / Braisted, A.C. / Randal, M. / Arkin, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nbp.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nbp.ent.gz | 26.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nbp_validation.pdf.gz | 717 KB | Display | wwPDB validaton report |
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Full document | 1nbp_full_validation.pdf.gz | 717.4 KB | Display | |
Data in XML | 1nbp_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1nbp_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/1nbp ftp://data.pdbj.org/pub/pdb/validation_reports/nb/1nbp | HTTPS FTP |
-Related structure data
Related structure data | 1m4aS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15375.948 Da / Num. of mol.: 1 / Mutation: Y31C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60568 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MHC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.34 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG 8k, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 17, 2001 / Details: mirrors |
Radiation | Monochromator: yale miorrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 7096 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.5 / Num. unique all: 715 / Rsym value: 0.253 / % possible all: 96.9 |
Reflection | *PLUS Lowest resolution: 10 Å |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M4A Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.077 / SU ML: 0.177 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.507 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.273 Å / Total num. of bins used: 15 /
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |