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Yorodumi- PDB-4gsc: Structure analysis of insulin degrading enzyme with compound bdm4... -
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-Basic information
Entry | Database: PDB / ID: 4gsc | ||||||
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Title | Structure analysis of insulin degrading enzyme with compound bdm41559 ((s)-2-[2-(carboxymethyl-phenethyl-amino)-acetylamino]-3-(1h-imidazol-4-yl)-propionic acid methyl ester) | ||||||
Components | Insulin-degrading enzyme | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / INSULIN DEGRADING ENZYME / 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 / insulin binding / regulation of aerobic respiration / peptide catabolic process ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / peptide binding / proteolysis involved in protein catabolic process / Peroxisomal protein import / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / virus receptor activity / positive regulation of protein binding / insulin receptor signaling pathway / peroxisome / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Guo, Q. / Deprez-Poulain, R. / Deprez, B. / Tang, W.J. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2014 Title: Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-beta hydrolysis. Authors: Charton, J. / Gauriot, M. / Guo, Q. / Hennuyer, N. / Marechal, X. / Dumont, J. / Hamdane, M. / Pottiez, V. / Landry, V. / Sperandio, O. / Flipo, M. / Buee, L. / Staels, B. / Leroux, F. / ...Authors: Charton, J. / Gauriot, M. / Guo, Q. / Hennuyer, N. / Marechal, X. / Dumont, J. / Hamdane, M. / Pottiez, V. / Landry, V. / Sperandio, O. / Flipo, M. / Buee, L. / Staels, B. / Leroux, F. / Tang, W.J. / Deprez, B. / Deprez-Poulain, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gsc.cif.gz | 402.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gsc.ent.gz | 320.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gsc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4gsc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4gsc_validation.xml.gz | 71.2 KB | Display | |
Data in CIF | 4gsc_validation.cif.gz | 96.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/4gsc ftp://data.pdbj.org/pub/pdb/validation_reports/gs/4gsc | HTTPS FTP |
-Related structure data
Related structure data | 2ypuC 3qz2C 4dttC 4dwkC 4gs8C 2wbyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 114560.578 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.) Homo sapiens (human) / Gene: IDE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14735, insulysin #2: Chemical | #3: Chemical | #4: 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: 4 Å3/Da / Density % sol: 69.25 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 10-13% PEG MME 5000, 100 MM HEPES PH 7.0, 4-14% TACSIMATE, 10% DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9597 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 19, 2010 |
Radiation | Monochromator: MAR 345 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9597 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→50 Å / Num. all: 79021 / Num. obs: 75029 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.81→2.9 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WBY Resolution: 2.81→49.85 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.381 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.677 / ESU R Free: 0.345 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→49.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.88 Å / Total num. of bins used: 20
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