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Yorodumi- PDB-5edb: human fatty acid binding protein 4 in complex with 6-Chloro-2-met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5edb | ||||||
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Title | human fatty acid binding protein 4 in complex with 6-Chloro-2-methyl-4-phenyl-quinoline-3-carboxylic acid at 1.18A | ||||||
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 / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / 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 / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / positive regulation of cold-induced thermogenesis / cellular response to tumor necrosis factor / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.18 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 | 5edb.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5edb.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 5edb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5edb_validation.pdf.gz | 782 KB | Display | wwPDB validaton report |
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Full document | 5edb_full_validation.pdf.gz | 783 KB | Display | |
Data in XML | 5edb_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 5edb_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/5edb ftp://data.pdbj.org/pub/pdb/validation_reports/ed/5edb | HTTPS FTP |
-Related structure data
Related structure data | 5edcC 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: 14965.123 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-265 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-5M8 / |
#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: 2.2 Å3/Da / Density % sol: 44.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES/NaOH pJ 7.5, 2-2.2 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: Jun 25, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.18→43.93 Å / Num. obs: 44284 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.13 % / Biso Wilson estimate: 17.249 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.048 / Χ2: 1.024 / Net I/σ(I): 18.31 / Num. measured all: 272461 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.18→37.7 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 59.94 Å2 / Biso mean: 17.3655 Å2 / Biso min: 8.52 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→37.7 Å
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