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- PDB-5d8j: Development of a therapeutic monoclonal antibody targeting secret... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d8j | ||||||
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Title | Development of a therapeutic monoclonal antibody targeting secreted aP2 to treat type 2 diabetes. | ||||||
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![]() | IMMUNE SYSTEM / AP2 / Fabp4 / Diabetes / metabolic syndrome | ||||||
Function / homology | ![]() Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process / cholesterol homeostasis / fatty acid binding / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Doyle, C. / Birrane, G. | ||||||
![]() | ![]() Title: Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes. Authors: Burak, M.F. / Inouye, K.E. / White, A. / Lee, A. / Tuncman, G. / Calay, E.S. / Sekiya, M. / Tirosh, A. / Eguchi, K. / Birrane, G. / Lightwood, D. / Howells, L. / Odede, G. / Hailu, H. / ...Authors: Burak, M.F. / Inouye, K.E. / White, A. / Lee, A. / Tuncman, G. / Calay, E.S. / Sekiya, M. / Tirosh, A. / Eguchi, K. / Birrane, G. / Lightwood, D. / Howells, L. / Odede, G. / Hailu, H. / West, S. / Garlish, R. / Neale, H. / Doyle, C. / Moore, A. / Hotamisligil, G.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.5 KB | Display | ![]() |
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PDB format | ![]() | 185.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 461.2 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14815.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23733.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 23515.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100mM 2-(N-morpholino)ethanesulfonic acid, 150mM ammonium sulfate, 24% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→33.03 Å / Num. obs: 13077 / % possible obs: 98.6 % / Observed criterion σ(I): 6.8 / Redundancy: 2.6 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.23→2.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.673 Å2
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Refinement step | Cycle: 1 / Resolution: 3→33.02 Å
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Refine LS restraints |
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