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Yorodumi- PDB-5edc: human FABP4 in complex with 6-Chloro-4-phenyl-2-piperidin-1-yl-qu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5edc | ||||||
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Title | human FABP4 in complex with 6-Chloro-4-phenyl-2-piperidin-1-yl-quinoline-3-carboxylic acid at 1.29A | ||||||
Components | Fatty acid-binding protein, adipocyte | ||||||
Keywords | LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING | ||||||
Function / homology | Function and homology information hormone receptor binding / white fat cell differentiation / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / long-chain fatty acid transport / Triglyceride catabolism / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / white fat cell differentiation / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / long-chain fatty acid transport / Triglyceride catabolism / 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 / Resolution: 1.29 Å | ||||||
Authors | Rudolph, M.G. / Ehler, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: A Real-World Perspective on Molecular Design. Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5edc.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5edc.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 5edc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5edc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5edc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5edc_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5edc_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/5edc ftp://data.pdbj.org/pub/pdb/validation_reports/ed/5edc | HTTPS FTP |
-Related structure data
Related structure data | 5edbC 5edeC 5edgC 5edhC 5ediC 5ezxC 5ezzC 5f00C 5f01C 5f02C 5f03C 5i2rC C: citing same article (ref.) |
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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: 14810.978 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 3-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090 | ||
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#2: Chemical | ChemComp-5M7 / | ||
#3: Chemical | #4: 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: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES/NaOH pH 7.5, 2.0-2.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.24→43.51 Å / Num. obs: 37129 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.08 % / Biso Wilson estimate: 22.666 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.037 / Net I/σ(I): 12.86 / Num. measured all: 228777 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.29→43.51 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.399 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.052 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 76.05 Å2 / Biso mean: 19.711 Å2 / Biso min: 12.6 Å2
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Refinement step | Cycle: final / Resolution: 1.29→43.51 Å
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LS refinement shell | Resolution: 1.29→1.323 Å / Total num. of bins used: 20
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