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- PDB-8rdp: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rdp | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8a | ||||||
![]() | Cereblon isoform 4 | ||||||
![]() | SIGNALING PROTEIN / CEREBLON / Ubiquitination / E3 / MOLECULAR GLUE / spiro-isoxazole | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / : / PHOSPHATE ION / Cereblon isoform 4![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bischof, L. / Hartmann, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode. Authors: Shevalev, R. / Bischof, L. / Sapegin, A. / Bunev, A. / Olga, G. / Kantin, G. / Kalinin, S. / Hartmann, M.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8rdqC ![]() 8rdrC ![]() 8rdsC ![]() 8rdtC C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 13703.577 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MGR_0879 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 96 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | Mass: 278.691 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM thalidomide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 11, 2023 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.0001 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.76→47.48 Å / Num. obs: 56873 / % possible obs: 100 % / Redundancy: 6.89 % / Biso Wilson estimate: 38.389 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.13 / Net I/σ(I): 8.06 | ||||||||||||||||||
Reflection shell | Rrim(I) all: 0.13 / Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.359 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→47.48 Å
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Refine LS restraints |
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