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- PDB-6s4i: Crystal structure of zinc free A14E, B25H, B29K(N(eps)-[2-(2-[2-(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s4i | ||||||
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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]), desB30 human insulin | ||||||
![]() | (Insulin![]() | ||||||
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Function / homology | ![]() Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 41.7 KB | Display | ![]() |
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PDB format | ![]() | 32.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 297 KB | Display | ![]() |
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Full document | ![]() | 297 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#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: 3323.822 Da / Num. of mol.: 1 / Mutation: F25H,des30 Source method: isolated from a genetically manipulated source Details: Insulin B chain LYS B29 CHEMICALLY MODIFIED WITH [2-(2-[2-(2-[2-(Octadecandioyl-gamma-Glu)amino]ethoxy)ethoxy]acetylamino)ethoxy]ethoxy)acetyl] Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64 % |
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Crystal grow![]() | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein solution: 25 mg/ml insulin added 0.1% (w/v) NVoy Precipitant: 6.0 M ammonium nitrate, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2009 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.511→31.63 Å / Num. obs: 12258 / % possible obs: 99.7 % / Redundancy: 25.2 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05816 / Rpim(I) all: 0.009455 / Rrim(I) all: 0.05896 / Net I/σ(I): 54.75 |
Reflection shell | Resolution: 1.511→1.565 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.5101 / Mean I/σ(I) obs: 4.25 / Num. unique obs: 1201 / CC1/2: 0.923 / Rpim(I) all: 0.1337 / Rrim(I) all: 0.5285 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.511→31.63 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: 20.629 Å / Origin y: 38.6419 Å / Origin z: 28.2937 Å
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Refinement TLS group | Selection details: all |