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- PDB-6qip: 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: 6qip | |||||||||
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Title | Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the albumin-biniding side chain of the human growth hormone derivative somapacitan | |||||||||
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![]() | TRANSPORT PROTEIN / complex / albumin binding / long-acting growth hormone / somapacitan / HORMONE | |||||||||
Function / homology | ![]() IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / IgG binding / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / IgG binding / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule binding / beta-2-microglobulin binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / 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 / 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 / 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 / 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 / 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 / positive regulation of cellular senescence / peptide antigen binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / tertiary granule lumen / Platelet degranulation / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / blood microparticle / endosome membrane / immune response / copper ion binding / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus 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 | ![]() | 207.7 KB | Display | ![]() |
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PDB format | ![]() | 161.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 535.7 KB | Display | ![]() |
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Full document | ![]() | 551 KB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qioC ![]() 4k71S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 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 , 5 types, 30 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/JG5.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/JG5.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MES / |
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#5: Chemical | ChemComp-JG5 / |
#6: Chemical | ChemComp-BME / |
#7: Chemical | ChemComp-CYS / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: sodium cacodylate, PEG3350 |
-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: Sep 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: 2.45→44.14 Å / Num. obs: 52497 / % possible obs: 99.91 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08365 / Rpim(I) all: 0.03514 / Rrim(I) all: 0.09086 / Net I/σ(I): 17.08 |
Reflection shell | Resolution: 2.45→2.538 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.683 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 5168 / CC1/2: 0.585 / Rpim(I) all: 0.7175 / Rrim(I) all: 1.831 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K71 Resolution: 2.45→46.479 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 31.2 / 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: 2.45→46.479 Å
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Refine LS restraints |
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LS refinement shell |
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