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- PDB-5d48: Crystal Structure of FABP4 in complex with 3-{5-cyclopropyl-3-(3,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d48 | ||||||
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Title | Crystal Structure of FABP4 in complex with 3-{5-cyclopropyl-3-(3,5-dimethyl-1H-pyrazol-4-yl)-2-[3-(propan-2-yloxy) phenyl]-1H-indol-1-yl}propanoic acid | ||||||
![]() | Fatty acid-binding protein, adipocyte | ||||||
![]() | LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN | ||||||
Function / homology | ![]() hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. ...Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. / Kashiwagi, T. / Ishikawa, K. / Miyano, H. / Mizukoshi, T. | ||||||
![]() | ![]() Title: Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis Authors: Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. / Kashiwagi, T. / Ishikawa, K. / Miyano, H. / Mizukoshi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.5 KB | Display | ![]() |
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Full document | ![]() | 839.6 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d45C ![]() 5d47C ![]() 5d4aC ![]() 2hnxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16911.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-L96 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.41 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 2.4 M NaH2PO4/K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 26, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.81→50 Å / Num. obs: 12310 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 18.4 % / Biso Wilson estimate: 25.359 Å2 / Rmerge F obs: 0.061 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Net I/σ(I): 18.92 / Num. measured all: 85078 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HNX Resolution: 1.81→43.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.1861 / FOM work R set: 0.8411 / SU B: 2.877 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1404 / SU Rfree: 0.1435 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 118.54 Å2 / Biso mean: 21.749 Å2 / Biso min: 10.62 Å2
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Refinement step | Cycle: final / Resolution: 1.81→43.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
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