+Open data
-Basic information
Entry | Database: PDB / ID: 3cww | ||||||
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Title | Crystal Structure of IDE-bradykinin complex | ||||||
Components |
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Keywords | HYDROLASE / A-beta degrading enzyme / criptidase / bradykinin / kinins | ||||||
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 / Resolution: 1.96 Å | ||||||
Authors | Malito, E. / Tang, W.J. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Molecular Bases for the Recognition of Short Peptide Substrates and Cysteine-Directed Modifications of Human Insulin-Degrading Enzyme Authors: Malito, E. / Ralat, L.A. / Manolopoulou, M. / Tsay, J.L. / Wadlington, N.L. / Tang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cww.cif.gz | 440.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cww.ent.gz | 346.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/3cww ftp://data.pdbj.org/pub/pdb/validation_reports/cw/3cww | HTTPS FTP |
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-Related structure data
Related structure data | 2jg4S 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
-Protein / Protein/peptide , 2 types, 4 molecules ABDE
#1: Protein | Mass: 113893.922 Da / Num. of mol.: 2 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, RP11-366I13.1-001, hCG_1810909 / Plasmid: pProEX-CF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P14735, insulysin #2: Protein/peptide | Mass: 354.400 Da / Num. of mol.: 2 / Fragment: N-terminal bradykinin Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 1710 molecules
#3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-DIO / #6: 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: 3.94 Å3/Da / Density % sol: 68.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 13% PEGMME 5000, 100mM HEPES, pH 7.0, 10%, Tacsimate, 10% dioxane, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 248865 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 28.08 Å2 / Rsym value: 0.088 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 23609 / Rsym value: 0.501 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Starting model: 2JG4 Resolution: 1.96→29.77 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 13.72 Å2 / Biso mean: 30.48 Å2 / Biso min: 85.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→29.77 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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