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Yorodumi- PDB-7k1d: Crystal structure of human insulin degrading enzyme (IDE) in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k1d | ||||||
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Title | Crystal structure of human insulin degrading enzyme (IDE) in complex with compound BDM_77291 | ||||||
Components | Insulin-degrading enzyme | ||||||
Keywords | HYDROLASE/HYDROLASE INHBITOR / Hydrolase / inhibitor / HYDROLASE-HYDROLASE INHBITOR 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 / 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 / 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: 3 Å | ||||||
Authors | Liang, W.G. / Deprez, R. / Bosc, D. / Tang, W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human insulin degrading enzyme (IDE) in complex with compound 2 Authors: Liang, W.G. / Deprez, R. / Bosc, D. / Tang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k1d.cif.gz | 410.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k1d.ent.gz | 322.4 KB | Display | PDB format |
PDBx/mmJSON format | 7k1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k1d_validation.pdf.gz | 1007.8 KB | Display | wwPDB validaton report |
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Full document | 7k1d_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7k1d_validation.xml.gz | 65.7 KB | Display | |
Data in CIF | 7k1d_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/7k1d ftp://data.pdbj.org/pub/pdb/validation_reports/k1/7k1d | HTTPS FTP |
-Related structure data
Related structure data | 4ifhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 114561.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDE Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P14735, insulysin #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-DIO / #5: Chemical | Has ligand of interest | Y | |
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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: 3.98 Å3/Da / Density % sol: 69.11 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG 5000, 100mM HEPES, 14% Tacsimate, 10% Dioxane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 106330 / % possible obs: 100 % / Observed criterion σ(I): 1.2 / Redundancy: 10.3 % / Biso Wilson estimate: 60.67 Å2 / CC1/2: 0.987 / CC star: 0.997 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 3→3.05 Å / Num. unique obs: 2735 / CC1/2: 0.46 / CC star: 0.794 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IFH Resolution: 3→45.42 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.41 / 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: 3→45.42 Å
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Refine LS restraints |
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LS refinement shell |
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