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- PDB-2wby: Crystal structure of human insulin-degrading enzyme in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wby | ||||||
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Title | Crystal structure of human insulin-degrading enzyme in complex with insulin | ||||||
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![]() | HYDROLASE/HORMONE / GLUCOSE METABOLISM / CARBOHYDRATE METABOLISM / DISEASE MUTATION / DIABETES MELLITUS / ZINC / DIOXANE / INSULIN / HORMONE / SECRETED / PROTEASE / DISULFIDE BOND / PHARMACEUTICAL / METALLOPROTEASE / HUMAN INSULIN-DEGRADNG ENZYME / HYDROLASE / CYTOPLASM / POLYMORPHISM / METAL-BINDING / CLEAVAGE ON PAIR OF BASIC RESIDUES / HYDROLASE-HORMONE complex | ||||||
Function / homology | ![]() insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / negative regulation of NAD(P)H oxidase activity ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / regulation of aerobic respiration / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / peptide catabolic process / IRS activation / Insulin processing / regulation of protein secretion / amyloid-beta clearance / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / peroxisomal matrix / 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 / amyloid-beta metabolic process / 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 / proteolysis involved in protein catabolic process / 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 / Peroxisomal protein import / regulation of transmembrane transporter activity / peptide binding / insulin-like growth factor receptor binding / wound healing / protein catabolic process / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / cognition / metalloendopeptidase activity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / positive regulation of protein catabolic process / vasodilation / peroxisome / glucose metabolic process / regulation of protein localization / positive regulation of protein binding / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / basolateral plasma membrane / secretory granule lumen Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Manolopoulou, M. / Guo, Q. / Malito, E. / Schilling, A.B. / Tang, W.J. | ||||||
![]() | ![]() Title: Molecular Basis of Catalytic Chamber-Assisted Unfolding and Cleavage of Human Insulin by Human Insulin Degrading Enzyme. Authors: Manolopoulou, M. / Guo, Q. / Malito, E. / Schilling, A.B. / Tang, W.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 428.8 KB | Display | ![]() |
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PDB format | ![]() | 341.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 273.9 KB | Display | ![]() |
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Full document | ![]() | 541 KB | Display | |
Data in CIF | ![]() | 110.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wc0C ![]() 2g47S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 114560.578 Da / Num. of mol.: 2 / Fragment: RESIDUES 42-1019 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2269.595 Da / Num. of mol.: 2 / Fragment: RESIDUES 90-109 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Protein/peptide | Mass: 2147.518 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-43 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 110 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLU 111 TO GLN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow | pH: 7 Details: 10-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jun 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 109017 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G47 Resolution: 2.6→32.08 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.876 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→32.08 Å
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