+Open data
-Basic information
Entry | Database: PDB / ID: 8wdx | ||||||
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Title | Crystal structure of human FABP4 complexed with C3 | ||||||
Components | Fatty acid-binding protein, adipocyte | ||||||
Keywords | LIPID BINDING PROTEIN/INHIBITOR / lipid binding protein-inhibitor complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Xie, H. / Chen, G.F. / Xu, Y.C. | ||||||
Funding support | 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Structure-based design of potent FABP4 inhibitors with high selectivity against FABP3. Authors: Chen, G. / Xie, H. / You, M. / Liu, J. / Shao, Q. / Li, M. / Su, H. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wdx.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wdx.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 8wdx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wdx_validation.pdf.gz | 781.7 KB | Display | wwPDB validaton report |
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Full document | 8wdx_full_validation.pdf.gz | 781.6 KB | Display | |
Data in XML | 8wdx_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 8wdx_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/8wdx ftp://data.pdbj.org/pub/pdb/validation_reports/wd/8wdx | HTTPS FTP |
-Related structure data
Related structure data | 8we3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 BL21(DE3) (bacteria) / References: UniProt: P15090 |
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#2: Chemical | ChemComp-W6K / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M trisodium citrate, PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→32.19 Å / Num. obs: 18385 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.65→1.709 Å / Num. unique obs: 1791 / CC1/2: 0.795 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.19 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→32.19 Å
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Refine LS restraints |
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LS refinement shell |
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