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Yorodumi- PDB-4re9: Crystal structure of human insulin degrading enzyme (IDE) in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4re9 | ||||||
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Title | Crystal structure of human insulin degrading enzyme (IDE) in complex with compound 71290 | ||||||
Components | Insulin-degrading enzyme | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / metalloendopeptidase activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / peroxisome / positive regulation of protein catabolic process / virus receptor activity / insulin receptor signaling pathway / positive regulation of protein binding / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å | ||||||
Authors | Liang, W.G. / Deprez, R. / Deprez, B. / Tang, W.J. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice. Authors: Deprez-Poulain, R. / Hennuyer, N. / Bosc, D. / Liang, W.G. / Enee, E. / Marechal, X. / Charton, J. / Totobenazara, J. / Berte, G. / Jahklal, J. / Verdelet, T. / Dumont, J. / Dassonneville, S. ...Authors: Deprez-Poulain, R. / Hennuyer, N. / Bosc, D. / Liang, W.G. / Enee, E. / Marechal, X. / Charton, J. / Totobenazara, J. / Berte, G. / Jahklal, J. / Verdelet, T. / Dumont, J. / Dassonneville, S. / Woitrain, E. / Gauriot, M. / Paquet, C. / Duplan, I. / Hermant, P. / Cantrelle, F.X. / Sevin, E. / Culot, M. / Landry, V. / Herledan, A. / Piveteau, C. / Lippens, G. / Leroux, F. / Tang, W.J. / van Endert, P. / Staels, B. / Deprez, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4re9.cif.gz | 410.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4re9.ent.gz | 326.2 KB | Display | PDB format |
PDBx/mmJSON format | 4re9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/4re9 ftp://data.pdbj.org/pub/pdb/validation_reports/re/4re9 | HTTPS FTP |
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-Related structure data
Related structure data | 4ifhC 4nxoC 3cwwS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 114561.562 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019 Mutation: C110L, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDE / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin |
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-Non-polymers , 7 types, 112 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 68.99 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG5000, 100 mM HEPES, 14% Tacsimate, 10% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 78800 / Num. obs: 78721 / % possible obs: 99.9 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.164 / Rsym value: 0.137 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.7 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CWW Resolution: 2.908→49.699 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 22.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.908→49.699 Å
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Refine LS restraints |
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LS refinement shell |
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