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- PDB-1qiy: HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qiy | ||||||
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Title | HUMAN INSULIN HEXAMERS WITH CHAIN B HIS MUTATED TO TYR COMPLEXED WITH PHENOL | ||||||
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![]() | HORMONE / GLUCOSE METABOLISM / DIABETES / INSULIN MUTANT | ||||||
Function / homology | ![]() negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / 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 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic 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 / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tang, L. / Whittingham, J.L. / Verma, C.S. / Caves, L.S.D. / Dodson, G.G. | ||||||
![]() | ![]() Title: Structural Consequences of the B5 Histidine --> Tyrosine Mutation in Human Insulin Characterized by X-Ray Crystallography and Conformational Analysis. Authors: Tang, L. / Whittingham, J.L. / Verma, C.S. / Caves, L.S.D. / Dodson, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77 KB | Display | ![]() |
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PDB format | ![]() | 58.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.6 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 13.6 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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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS A 2ZN INSULIN HEXAMER,CONSISTING OF THREE EQUIVALENT DIMERS RELATED BY A NON-CRYSTALLOGRAPHIC 3-FOLD SYMMETRY AXIS. THE ZINC AND CHLORIDE IONS ARE LOCATED ON THIS 3-FOLD AXIS. |
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Components
-Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3458.980 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 101 molecules ![](data/chem/img/IPH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IPH / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN B, HIS 29 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 29 TO TYR ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: CRYSTALLISATION IN BATCH, 10 MG B5 TYR INSULIN DISSOLVED IN 2 ML 0.02M HCL. TO THIS ADDED 0.1 ML 0.12M ZINC ACETATE, 1.5 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 2.5% (AQ.) PHENOL AND 120 MG NACL. ...Details: CRYSTALLISATION IN BATCH, 10 MG B5 TYR INSULIN DISSOLVED IN 2 ML 0.02M HCL. TO THIS ADDED 0.1 ML 0.12M ZINC ACETATE, 1.5 ML 0.2 M TRI-SODIUM CITRATE, 0.4 ML 2.5% (AQ.) PHENOL AND 120 MG NACL. PH ADJUSTED TO 6.5-7.8 . | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / PH range low: 7.8 / PH range high: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ![]() |
Detector | Type: MULTIWIRE SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→36.8 Å / Num. obs: 13832 / % possible obs: 92 % / Redundancy: 1.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 5 / % possible all: 95.5 |
Reflection shell | *PLUS % possible obs: 95.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: R6 (NATIVE) INSULIN Resolution: 2.3→36.8 Å / σ(F): 0 Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, A4, A14, B13, B21, B29, B30, C4, D1, E5, F1, F21, F25, G4, H13, H21, J21, L1, L21, L30 THE FOLLOWING CHAIN ...Details: THE FOLLOWING SIDECHAINS HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, A4, A14, B13, B21, B29, B30, C4, D1, E5, F1, F21, F25, G4, H13, H21, J21, L1, L21, L30 THE FOLLOWING CHAIN TERMINAL RESIDUES HAVE BEEN ASSIGNED ZERO OCCUPANCIES DUE TO DISORDER, D29-D30, F29-F30, H29-H30, J29-J30
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Displacement parameters | Biso mean: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→36.8 Å
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