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Yorodumi- PDB-5d4a: Crystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d4a | ||||||
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Title | Crystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1-yl)propanoic acid | ||||||
Components | Fatty acid-binding protein, adipocyte | ||||||
Keywords | LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d4a.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d4a.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 5d4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d4a_validation.pdf.gz | 820.4 KB | Display | wwPDB validaton report |
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Full document | 5d4a_full_validation.pdf.gz | 821.6 KB | Display | |
Data in XML | 5d4a_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5d4a_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/5d4a ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d4a | HTTPS FTP |
-Related structure data
Related structure data | 5d45C 5d47C 5d48C 2hnxS C: citing same article (ref.) 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: 16911.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P15090 |
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#2: Chemical | ChemComp-57Q / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.17 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 18, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 16778 / % possible obs: 95.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.064 / Χ2: 1.846 / Net I/av σ(I): 39.656 / Net I/σ(I): 15.3 / Num. measured all: 106879 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HNX Resolution: 1.7→43.53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.113 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / 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 mean: 22.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→43.53 Å
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Refine LS restraints |
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