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- PDB-6e5l: Crystal structure of human cellular retinol binding protein 1 in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6e5l | ||||||
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Title | Crystal structure of human cellular retinol binding protein 1 in complex with abnormal-cannabidiol (abn-CBD) | ||||||
![]() | Retinol-binding protein 1 | ||||||
![]() | LIPID BINDING PROTEIN / vitamin A / retinol / abn-CBD / abnormal cannabidiol | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silvaroli, J.A. / Banerjee, S. / Kiser, P.D. / Golczak, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Abnormal Cannabidiol Modulates Vitamin A Metabolism by Acting as a Competitive Inhibitor of CRBP1. Authors: Silvaroli, J.A. / Widjaja-Adhi, M.A.K. / Trischman, T. / Chelstowska, S. / Horwitz, S. / Banerjee, S. / Kiser, P.D. / Blaner, W.S. / Golczak, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 841.1 KB | Display | ![]() |
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Full document | ![]() | 841 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e5tC ![]() 6e5wC ![]() 6e6kC ![]() 6e6mC ![]() 5h8tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16568.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HVD / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BisTris, pH 5.5, and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: CCD / Date: Nov 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→46.07 Å / Num. obs: 47869 / % possible obs: 99.3 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rpim(I) all: 0.05 / Rsym value: 0.12 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.17→1.19 Å / Mean I/σ(I) obs: 5.5 / Num. unique obs: 2384 / CC1/2: 0.69 / Rsym value: 0.6 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5H8T Resolution: 1.17→46.07 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→46.07 Å
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Refine LS restraints |
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LS refinement shell |
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