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Yorodumi- PDB-7g0b: Crystal Structure of human FABP5 in complex with 7-bromo-1-methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7g0b | ||||||
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Title | Crystal Structure of human FABP5 in complex with 7-bromo-1-methyl-5-phenyl-2,3,4,5-tetrahydro-1-benzazepine-4-carboxylic acid | ||||||
Components | Fatty acid-binding protein 5 | ||||||
Keywords | LIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING | ||||||
Function / homology | Function and homology information regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / lipid binding / synapse / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Ehler, A. / Benz, J. / Obst, U. / Ceccarelli-Simona, M. / Rudolph, M.G. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To be published Title: Crystal Structure of a human FABP5 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 | 7g0b.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7g0b.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 7g0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/7g0b ftp://data.pdbj.org/pub/pdb/validation_reports/g0/7g0b | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15467.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01469 |
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#2: Chemical | ChemComp-DMS / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-WK0 / ( |
#5: 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: 2.34 Å3/Da / Density % sol: 47.52 % |
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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: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→47.84 Å / Num. obs: 25705 / % possible obs: 99.9 % / Redundancy: 12.704 % / Biso Wilson estimate: 32.196 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.052 / Χ2: 0.864 / Net I/σ(I): 23.7 / Num. measured all: 326562 / Scaling rejects: 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.47→47.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.483 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: bromine partially radiolyzed methyl group not visible in electron density both chiral centers are S
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80 Å2 / Biso mean: 27.984 Å2 / Biso min: 18.95 Å2
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Refinement step | Cycle: final / Resolution: 1.47→47.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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