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Yorodumi- PDB-7g14: Crystal Structure of human FABP4 in complex with 6-cyclopentyl-N,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7g14 | ||||||
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Title | Crystal Structure of human FABP4 in complex with 6-cyclopentyl-N,5-dimethyl-4-phenyl-N-propan-2-yl-3-(1H-tetrazol-5-yl)pyridin-2-amine | ||||||
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 / 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: 1.2 Å | ||||||
Authors | Ehler, A. / Benz, J. / Obst, U. / Kuhne, H. / Rudolph, M.G. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To be published Title: Crystal Structure of a human FABP4 complex Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7g14.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7g14.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 7g14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7g14_validation.pdf.gz | 822.8 KB | Display | wwPDB validaton report |
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Full document | 7g14_full_validation.pdf.gz | 823.9 KB | Display | |
Data in XML | 7g14_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7g14_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/7g14 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/7g14 | HTTPS FTP |
-Group deposition
ID | G_1002264 (222 entries) |
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Title | To be published |
Type | undefined |
Description | A set of fabp crystal structures |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15022.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090 |
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-Non-polymers , 5 types, 134 molecules
#2: Chemical | #3: Chemical | ChemComp-Q1I / ( | #4: Chemical | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→30.77 Å / Num. obs: 41217 / % possible obs: 98.9 % / Redundancy: 5.99 % / Biso Wilson estimate: 19.708 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.037 / Rsym value: 0.034 / Χ2: 0.876 / Net I/σ(I): 20.85 / Num. measured all: 247967 / Scaling rejects: 29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: inhouse model Resolution: 1.2→30.79 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.372 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: isopropyl-methyl-amine not well defined, amine N is likely more pyramidal than built. this substituent is, however, slightly better defined compared to FABP4_5.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.32 Å2 / Biso mean: 19.251 Å2 / Biso min: 9.45 Å2
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Refinement step | Cycle: final / Resolution: 1.2→30.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.204→1.235 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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