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- PDB-4pf9: Crystal structure of insulin degrading enzyme complexed with inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pf9 | ||||||
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Title | Crystal structure of insulin degrading enzyme complexed with inhibitor | ||||||
![]() | Insulin-degrading enzyme | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / HYDROLASE-HYDROLASE INHIBITOR 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 / regulation of aerobic respiration ...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 / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / proteolysis involved in protein catabolic process / Peroxisomal protein import / peptide binding / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / peroxisome / positive regulation of protein binding / insulin receptor signaling pathway / virus receptor activity / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Guo, S. | ||||||
![]() | ![]() Title: Dual Exosite-binding Inhibitors of Insulin-degrading Enzyme Challenge Its Role as the Primary Mediator of Insulin Clearance in Vivo. Authors: Durham, T.B. / Toth, J.L. / Klimkowski, V.J. / Cao, J.X. / Siesky, A.M. / Alexander-Chacko, J. / Wu, G.Y. / Dixon, J.T. / McGee, J.E. / Wang, Y. / Guo, S.Y. / Cavitt, R.N. / Schindler, J. / ...Authors: Durham, T.B. / Toth, J.L. / Klimkowski, V.J. / Cao, J.X. / Siesky, A.M. / Alexander-Chacko, J. / Wu, G.Y. / Dixon, J.T. / McGee, J.E. / Wang, Y. / Guo, S.Y. / Cavitt, R.N. / Schindler, J. / Thibodeaux, S.J. / Calvert, N.A. / Coghlan, M.J. / Sindelar, D.K. / Christe, M. / Kiselyov, V.V. / Michael, M.D. / Sloop, K.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 411.5 KB | Display | ![]() |
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PDB format | ![]() | 326 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 889.6 KB | Display | ![]() |
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Full document | ![]() | 903.9 KB | Display | |
Data in XML | ![]() | 66.9 KB | Display | |
Data in CIF | ![]() | 93.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pf7C ![]() 4pfcC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 114493.484 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019 Mutation: C110L, E111Q, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2 mM sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 71156 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 55.38 Å2 / Rsym value: 0.109 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.7 / % possible all: 99.2 |
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Processing
Software | Name: BUSTER / Version: 2.11.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2G47 Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.8861 / SU R Cruickshank DPI: 0.559 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.497 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.29
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Displacement parameters | Biso mean: 46.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.321 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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