[English] 日本語
Yorodumi- PDB-5d45: Crystal Structure of FABP4 in complex with 3-(5-cyclopropyl-2,3-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d45 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of FABP4 in complex with 3-(5-cyclopropyl-2,3-diphenyl-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: 1.65 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5d45.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5d45.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 5d45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d45_validation.pdf.gz | 798.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5d45_full_validation.pdf.gz | 800.6 KB | Display | |
Data in XML | 5d45_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 5d45_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/5d45 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d45 | HTTPS FTP |
-Related structure data
Related structure data | 5d47C 5d48C 5d4aC 2hnxS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-57P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.42 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 2.4 M NaH2PO4/K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 16156 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 18.78 % / Biso Wilson estimate: 23.032 Å2 / Rmerge F obs: 0.054 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.048 / Net I/σ(I): 28.34 / Num. measured all: 111887 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HNX Resolution: 1.65→43.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2066 / WRfactor Rwork: 0.1825 / FOM work R set: 0.8607 / SU B: 1.931 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1076 / SU Rfree: 0.1028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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 max: 65.64 Å2 / Biso mean: 18.294 Å2 / Biso min: 8.53 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→43.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
|