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- PDB-6qio: Ternary complex of FcRn ectodomain, FcRn binding optimised human ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qio | |||||||||
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Title | Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the human growth hormone derivative somapacitan | |||||||||
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![]() | HORMONE / complex / albumin binding / long-acting growth hormone / somapacitan | |||||||||
Function / homology | ![]() growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / positive regulation of growth / animal organ development / positive regulation of activation of Janus kinase activity / cellular response to calcium ion starvation / positive regulation of multicellular organism growth ...growth hormone activity / growth hormone receptor complex / bone maturation / prolactin receptor binding / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / positive regulation of growth / animal organ development / positive regulation of activation of Janus kinase activity / cellular response to calcium ion starvation / positive regulation of multicellular organism growth / exogenous protein binding / Ciprofloxacin ADME / positive regulation of glucose transmembrane transport / enterobactin binding / Heme biosynthesis / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor binding / IgG binding / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / growth hormone receptor signaling pathway / Heme degradation / Aspirin ADME / Prolactin receptor signaling / antioxidant activity / cell surface receptor signaling pathway via JAK-STAT / toxic substance binding / Synthesis, secretion, and deacylation of Ghrelin / small molecule binding / beta-2-microglobulin binding / Scavenging of heme from plasma / Growth hormone receptor signaling / Recycling of bile acids and salts / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to starvation / response to nutrient levels / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / platelet alpha granule lumen / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cytokine activity / endosome lumen / fatty acid binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of MAP kinase activity / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / hormone activity / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / cytokine-mediated signaling pathway / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / pyridoxal phosphate binding / positive regulation of protein binding / Platelet degranulation / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / response to estradiol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Johansson, E. | |||||||||
![]() | ![]() Title: Identification of Binding Sites on Human Serum Albumin for Somapacitan, a Long-Acting Growth Hormone Derivative. Authors: Johansson, E. / Nielsen, A.D. / Demuth, H. / Wiberg, C. / Schjodt, C.B. / Huang, T. / Chen, J. / Jensen, S. / Petersen, J. / Thygesen, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394.3 KB | Display | ![]() |
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PDB format | ![]() | 319.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523.3 KB | Display | ![]() |
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Full document | ![]() | 539.4 KB | Display | |
Data in XML | ![]() | 46.9 KB | Display | |
Data in CIF | ![]() | 69.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qipC ![]() 4k71S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 66473.148 Da / Num. of mol.: 1 / Mutation: V418M, T420A, E505G, V547A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 Production host: ![]() |
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#2: Protein | Mass: 30408.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 12577.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 4 types, 882 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/JG5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYS.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MES / | ||||
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#5: Chemical | #6: Chemical | ChemComp-JG5 / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: ammonium acetate, sodium acetate, PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.85 Å / Num. obs: 95478 / % possible obs: 99.91 % / Redundancy: 6.7 % / Net I/σ(I): 11.23 |
Reflection shell | Resolution: 1.95→2.02 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K71 Resolution: 1.95→48.846 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 23.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.846 Å
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Refine LS restraints |
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LS refinement shell |
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