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Yorodumi- PDB-4azm: Human epidermal fatty acid-binding protein (FABP5) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4azm | ||||||
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Title | Human epidermal fatty acid-binding protein (FABP5) in complex with the inhibitor BMS-309413 | ||||||
Components | FATTY ACID-BINDING PROTEIN, EPIDERMAL | ||||||
Keywords | LIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / ENDOCANNABINOID / BETA-BARREL / BETA-CLAMSHELL / DOMAIN SWAPPING | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Sanson, B. / Wang, T. / Sun, J. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic Study of Fabp5 as an Intracellular Endocannabinoid Transporter. Authors: Sanson, B. / Wang, T. / Sun, J. / Wang, L. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4azm.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4azm.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 4azm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4azm_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4azm_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4azm_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4azm_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4azm ftp://data.pdbj.org/pub/pdb/validation_reports/az/4azm | HTTPS FTP |
-Related structure data
Related structure data | 4aznC 4azoC 4azpC 4azqC 4azrC 1b56S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15467.732 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EPIDERMIS / Cell: KERATINOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01469 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | ADDITIONAL | |
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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.32 M SODIUM CITRATE, 0.1 M HEPES PH 7.0, SATURATED WITH RESPECT TO BMS-309403, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYOPROTECTION: 28% GLYCEROL IN MOTHER LIQUOR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2011 |
Radiation | Monochromator: DOUBLE SILICON(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→20 Å / Num. obs: 8919 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 72.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B56 Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 28.966 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.217 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
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Refine LS restraints |
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