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Yorodumi- PDB-8gey: Crystal structure of human cellular retinol binding protein 1 in ... -
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-Basic information
Entry | Database: PDB / ID: 8gey | |||||||||
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Title | Crystal structure of human cellular retinol binding protein 1 in complex with 4-(hydroxymethyl)-1-[(4-methoxy-5,6,7,8-tetrahydronaphthalen-1-yl)sulfonyl]piperidin-4-ol | |||||||||
Components | Retinol-binding protein 1 | |||||||||
Keywords | Retinol-binding protein / RBP1 / CRBP1 / retinol-binding / retinol / vitamin A | |||||||||
Function / homology | Function and homology information all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Plau, J. / Golczak, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms. Authors: Plau, J. / Morgan, C.E. / Fedorov, Y. / Banerjee, S. / Adams, D.J. / Blaner, W.S. / Yu, E.W. / Golczak, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gey.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gey.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gey_validation.pdf.gz | 742.4 KB | Display | wwPDB validaton report |
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Full document | 8gey_full_validation.pdf.gz | 742.9 KB | Display | |
Data in XML | 8gey_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 8gey_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/8gey ftp://data.pdbj.org/pub/pdb/validation_reports/ge/8gey | HTTPS FTP |
-Related structure data
Related structure data | 8gd2C 8gdmC 8gemC 8geuC 8gevC 6e5lS C: citing same article (ref.) S: Starting model for refinement |
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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: 16700.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE / References: UniProt: P09455 |
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#2: Chemical | ChemComp-ZE2 / |
#3: Chemical | ChemComp-BTB / |
#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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris, pH 5.5 and 25% poly ethylene glycol 3350 (w/v) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→43.02 Å / Num. obs: 36077 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 11.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.045 / Rrim(I) all: 0.11 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2 / Num. unique obs: 1765 / CC1/2: 0.67 / Rpim(I) all: 0.512 / Rrim(I) all: 0.641 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E5L Resolution: 1.3→38.75 Å / SU ML: 0.1026 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.1743 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→38.75 Å
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Refine LS restraints |
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LS refinement shell |
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