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Yorodumi- PDB-5mj6: Ligand-induced conformational change of Insulin-regulated aminope... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mj6 | ||||||||||||
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Title | Ligand-induced conformational change of Insulin-regulated aminopeptidase: insights on catalytic mechanism and active site plasticity. | ||||||||||||
Components | Leucyl-cystinyl aminopeptidase | ||||||||||||
Keywords | HYDROLASE / Insulin-regulated aminopeptidase / Endoplasmatic Reticulum Aminopeptidases / generation of antigenic peptides for cross-presentation / phosphinic pseudotripeptides / ligand-induced conformational changes | ||||||||||||
Function / homology | Function and homology information cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / Translocation of SLC2A4 (GLUT4) to the plasma membrane / female pregnancy / Endosomal/Vacuolar pathway ...cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / Translocation of SLC2A4 (GLUT4) to the plasma membrane / female pregnancy / Endosomal/Vacuolar pathway / peptide binding / cytoplasmic vesicle membrane / protein catabolic process / regulation of blood pressure / protein polyubiquitination / metallopeptidase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell-cell signaling / lysosomal membrane / perinuclear region of cytoplasm / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||||||||
Authors | Mpakali, A. / Stratikos, E. / Saridakis, E. / Giastas, P. | ||||||||||||
Funding support | United Kingdom, Greece, United States, 3items
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Citation | Journal: J. Med. Chem. / Year: 2017 Title: Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity. Authors: Mpakali, A. / Saridakis, E. / Harlos, K. / Zhao, Y. / Kokkala, P. / Georgiadis, D. / Giastas, P. / Papakyriakou, A. / Stratikos, E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mj6.cif.gz | 394 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mj6.ent.gz | 318.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mj6_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
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Full document | 5mj6_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 5mj6_validation.xml.gz | 67 KB | Display | |
Data in CIF | 5mj6_validation.cif.gz | 93.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mj6 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mj6 | HTTPS FTP |
-Related structure data
Related structure data | 2yd0S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 101182.039 Da / Num. of mol.: 2 / Fragment: UNP residues 155-1025 Source method: isolated from a genetically manipulated source Details: R is from the cloning, TETSQVAPA is the Rho1D4 tag / Source: (gene. exp.) Homo sapiens (human) / Gene: LNPEP, OTASE / Details (production host): TETSQVAPA is the Rho1D4 tag / Cell (production host): transformed with adenovirus 5 DNA / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney / References: UniProt: Q9UIQ6, cystinyl aminopeptidase |
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-Sugars , 5 types, 28 molecules
#2: Polysaccharide | #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 265 molecules
#7: Chemical | #8: Chemical | #9: Chemical | ChemComp-BR / #10: 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: 2.39 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18.8% (w/v) PEG of mean MW 20000, 37.6% (v/v) PEG monomethyl ether of mean MW 500, 50.2 mM Bicine, 43.8 mM Trizma base (pH of buffer mixture: 8.5) and 0.282 M each of the following halogens: ...Details: 18.8% (w/v) PEG of mean MW 20000, 37.6% (v/v) PEG monomethyl ether of mean MW 500, 50.2 mM Bicine, 43.8 mM Trizma base (pH of buffer mixture: 8.5) and 0.282 M each of the following halogens: Sodium fluoride, Sodium bromide and Sodium iodide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→40.805 Å / Num. obs: 80735 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 45.968 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.199 / Net I/σ(I): 0.812 |
Reflection shell | Resolution: 2.53→2.6 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.6 / CC1/2: 0.451 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YD0 Resolution: 2.53→40.805 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.54 / 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: 2.53→40.805 Å
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Refine LS restraints |
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LS refinement shell |
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