+Open data
-Basic information
Entry | Database: PDB / ID: 2il6 | ||||||
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Title | HUMAN INTERLEUKIN-6, NMR, 32 STRUCTURES | ||||||
Components | INTERLEUKIN-6 | ||||||
Keywords | CYTOKINE / GLYCOPROTEIN / GROWTH FACTOR | ||||||
Function / homology | Function and homology information positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation ...positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / positive regulation of type B pancreatic cell apoptotic process / regulation of microglial cell activation / hepatocyte proliferation / neutrophil apoptotic process / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / neutrophil mediated immunity / negative regulation of lipid storage / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / interleukin-6-mediated signaling pathway / maintenance of blood-brain barrier / Interleukin-6 signaling / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / monocyte chemotaxis / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / regulation of insulin secretion / positive regulation of glial cell proliferation / positive regulation of interleukin-10 production / humoral immune response / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / positive regulation of chemokine production / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / liver regeneration / positive regulation of smooth muscle cell proliferation / positive regulation of interleukin-1 beta production / response to activity / cytokine activity / acute-phase response / positive regulation of interleukin-8 production / positive regulation of translation / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of DNA-binding transcription factor activity / growth factor activity / platelet activation / cellular response to virus / negative regulation of neurogenesis / cytokine-mediated signaling pathway / cellular response to hydrogen peroxide / neuron cellular homeostasis / ADORA2B mediated anti-inflammatory cytokines production / positive regulation of interleukin-6 production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / positive regulation of tumor necrosis factor production / neuron projection development / glucose homeostasis / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to virus / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / negative regulation of cell population proliferation / endoplasmic reticulum lumen / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING. | ||||||
Authors | Xu, G.Y. / Yu, H.A. / Hong, J. / Stahl, M. / Mcdonagh, T. / Kay, L.E. / Cumming, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Solution structure of recombinant human interleukin-6. Authors: Xu, G.Y. / Yu, H.A. / Hong, J. / Stahl, M. / McDonagh, T. / Kay, L.E. / Cumming, D.A. #1: Journal: J.Biomol.NMR / Year: 1996 Title: Complete 1H, 15N and 13C Assignments, Secondary Structure, and Topology of Recombinant Human Interleukin-6 Authors: Xu, G.Y. / Hong, J. / Mcdonagh, T. / Stahl, M. / Kay, L.E. / Seehra, J. / Cumming, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2il6.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2il6.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 2il6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2il6_validation.pdf.gz | 349.2 KB | Display | wwPDB validaton report |
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Full document | 2il6_full_validation.pdf.gz | 735.1 KB | Display | |
Data in XML | 2il6_validation.xml.gz | 135.9 KB | Display | |
Data in CIF | 2il6_validation.cif.gz | 176.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/2il6 ftp://data.pdbj.org/pub/pdb/validation_reports/il/2il6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 21005.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05231 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 6.1 / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITY PLUS 600 / Manufacturer: Varian / Model: UNITY PLUS 600 / Field strength: 600 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING. / Software ordinal: 1 Details: STRUCTURES ARE BASED ON 2961 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NMR MEASUREMENTS INCLUDING 138 HYDROGEN BOND RESTRAINTS FROM 69 HYDROGEN BONDS IDENTIFIED USING AMIDE EXCHANGE DATA ...Details: STRUCTURES ARE BASED ON 2961 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NMR MEASUREMENTS INCLUDING 138 HYDROGEN BOND RESTRAINTS FROM 69 HYDROGEN BONDS IDENTIFIED USING AMIDE EXCHANGE DATA AND INITIAL STRUCTURE CALCULATIONS. IN ADDITION, 83 PHI BACKBONE TORSION ANGLE RESTRAINTS WERE DERIVED FROM COUPLING CONSTANTS. THE METHOD USED TO DERIVE THE FINAL ENSEMBLE OF STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M. NILGES, G.M. CLORE, AND A.M. GRONENBORN (1988) FEBS LETT. 229, 317-324. | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 75 / Conformers submitted total number: 32 |