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Yorodumi- PDB-2nnq: Crystal structure of human adipocyte fatty acid binding protein i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nnq | ||||||
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Title | Crystal structure of human adipocyte fatty acid binding protein in complex with ((2'-(5-ethyl-3,4-diphenyl-1H-pyrazol-1-yl)-3-biphenylyl)oxy)acetic acid | ||||||
Components | Fatty acid-binding protein, adipocyte | ||||||
Keywords | LIPID TRANSPORT / TRANSPORT / LIPID-BINDING | ||||||
Function / homology | Function and homology information hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / positive regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Jacobson, B.L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Potent and selective biphenyl azole inhibitors of adipocyte fatty acid binding protein (aFABP). Authors: Sulsky, R. / Magnin, D.R. / Huang, Y. / Simpkins, L. / Taunk, P. / Patel, M. / Zhu, Y. / Stouch, T.R. / Bassolino-Klimas, D. / Parker, R. / Harrity, T. / Stoffel, R. / Taylor, D.S. / Lavoie, ...Authors: Sulsky, R. / Magnin, D.R. / Huang, Y. / Simpkins, L. / Taunk, P. / Patel, M. / Zhu, Y. / Stouch, T.R. / Bassolino-Klimas, D. / Parker, R. / Harrity, T. / Stoffel, R. / Taylor, D.S. / Lavoie, T.B. / Kish, K. / Jacobson, B.L. / Sheriff, S. / Adam, L.P. / Ewing, W.R. / Robl, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nnq.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nnq.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 2nnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/2nnq ftp://data.pdbj.org/pub/pdb/validation_reports/nn/2nnq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14608.702 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 | #3: Chemical | ChemComp-T4B / (( | #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: 2.25 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Temperature: 293 K / pH: 5.6 Details: ~70% saturated ammonium sulfate, pH 5.6, vapor diffusion, hanging drop, temperature 293K, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: BRUKER / Detector: AREA DETECTOR / Date: Apr 22, 1999 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→99 Å / Num. obs: 12558 / % possible obs: 78.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.77→1.91 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 3.3 / % possible all: 64.9 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: AP2 Resolution: 1.8→5.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2022639.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 73.1434 Å2 / ksol: 0.564375 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→5.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
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Xplor file |
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