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- PDB-8gdm: 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: 8gdm | |||||||||
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Title | Crystal structure of human cellular retinol binding protein 1 in complex with {[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}(methyl)[1-(thiophen-2-yl)ethyl]amine | |||||||||
![]() | Retinol-binding protein 1 | |||||||||
![]() | Retinol-binding protein / RBP1 / CRBP1 / retinol-binding / retinol / vitamin A | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Plau, J. / Golczak, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.8 KB | Display | ![]() |
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PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739 KB | Display | ![]() |
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Full document | ![]() | 739.6 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gd2C ![]() 8gemC ![]() 8geuC ![]() 8gevC ![]() 8geyC ![]() 6e5lS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 16700.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZA6 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.03 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→94.03 Å / Num. obs: 13005 / % possible obs: 97.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.056 / Rrim(I) all: 0.088 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 737 / CC1/2: 0.764 / Rpim(I) all: 0.588 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6E5L Resolution: 1.8→36.04 Å / SU ML: 0.255 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.1237 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: 37.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.04 Å
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Refine LS restraints |
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LS refinement shell |
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