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- PDB-6s4j: Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(... -
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Basic information
Entry | Database: PDB / ID: 6s4j | ||||||
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Title | Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl]), desB27, desB30 human insulin | ||||||
![]() | (Insulin) x 2 | ||||||
![]() | HORMONE / insulin / oral / zinc free | ||||||
Function / homology | ![]() negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johansson, E. | ||||||
![]() | ![]() Title: Molecular engineering of safe and efficacious oral basal insulin. Authors: Hubalek, F. / Refsgaard, H.H.F. / Gram-Nielsen, S. / Madsen, P. / Nishimura, E. / Munzel, M. / Brand, C.L. / Stidsen, C.E. / Claussen, C.H. / Wulff, E.M. / Pridal, L. / Ribel, U. / ...Authors: Hubalek, F. / Refsgaard, H.H.F. / Gram-Nielsen, S. / Madsen, P. / Nishimura, E. / Munzel, M. / Brand, C.L. / Stidsen, C.E. / Claussen, C.H. / Wulff, E.M. / Pridal, L. / Ribel, U. / Kildegaard, J. / Porsgaard, T. / Johansson, E. / Steensgaard, D.B. / Hovgaard, L. / Glendorf, T. / Hansen, B.F. / Jensen, M.K. / Nielsen, P.K. / Ludvigsen, S. / Rugh, S. / Garibay, P.W. / Moore, M.C. / Cherrington, A.D. / Kjeldsen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.4 KB | Display | ![]() |
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PDB format | ![]() | 36 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6s4iSC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2349.638 Da / Num. of mol.: 1 / Mutation: Y14E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3222.718 Da / Num. of mol.: 1 / Mutation: F25H,des27,des30 Source method: isolated from a genetically manipulated source Details: LYS B30 covalently attached to [2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl] Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-IMD / |
#4: Chemical | ChemComp-KUT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.12M monosaccharides, 0.1M buffer system 1 pH 6.5, 20% (v/v) PEG500MME, 10% (w/v) Peg 20000 (F1 from Marpheus screen, Molecular Dimensions) |
-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: May 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.884 Å / Num. obs: 8938 / % possible obs: 99.85 % / Redundancy: 9.3 % / Biso Wilson estimate: 21.61 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05618 / Rpim(I) all: 0.01939 / Rrim(I) all: 0.05951 / Net I/σ(I): 21.02 |
Reflection shell | Resolution: 1.5→1.554 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.635 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 861 / CC1/2: 0.6 / Rpim(I) all: 0.6144 / Rrim(I) all: 1.75 / % possible all: 98.85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6S4I Resolution: 1.5→45.88 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.65 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -34.6332 Å / Origin y: 19.4109 Å / Origin z: 55.916 Å
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Refinement TLS group | Selection details: all |