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Yorodumi- PDB-2ws6: Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hex... -
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-Basic information
Entry | Database: PDB / ID: 2ws6 | ||||||
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Title | Semi-synthetic analogue of human insulin NMeTyrB26-insulin in hexamer form | ||||||
Components |
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Keywords | HORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / ANALOGUE / DIABETES MELLITUS | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / 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 / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Brzozowski, A.M. / Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Implications for the Active Form of Human Insulin Based on the Structural Convergence of Highly Active Hormone Analogues. Authors: Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G. / Brzozowski, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ws6.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ws6.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ws6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/2ws6 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/2ws6 | HTTPS FTP |
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-Related structure data
Related structure data | 2wruC 2wrvC 2wrwC 2wrxC 2ws0C 2ws1C 2ws4C 2ws7C 1msoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein/peptide , 3 types, 12 molecules ACEGIKBDFHJL
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: A CHAIN OF HUMAN INSULIN / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #3: Protein/peptide | Mass: 3447.979 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: METHYLATION OF TYROSINE RESIDUE 26 NITROGEN ATOM OF HUMAN INSULIN Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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-Non-polymers , 5 types, 255 molecules
#4: Chemical | ChemComp-IPH / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | ZINC (ZN): ZINC CATION CHLORINE (CL): CHLORINE ANION |
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Sequence details | N ATOM OF 26Y PEPTIDE IS METHYLATED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 6% TRIS PH 8.2, 0.1 M NA CITRATE, 0.02% ZN ACETATE, 0.06% PHENOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 50473 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MSO Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.533 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. A14, B21, C4, D1, I4, I14, L1 SIDE CHAINS OCCUPANCIES ARE SET TO ZERO DUE TO HIGH MOBILITY OF THESE SIDE CHAINS. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. A14, B21, C4, D1, I4, I14, L1 SIDE CHAINS OCCUPANCIES ARE SET TO ZERO DUE TO HIGH MOBILITY OF THESE SIDE CHAINS. B27-B30, D28-D30 F30, H28-H30, L28-L30 ARE NOT MODELLED DUE TO DISORDER.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.661 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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