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Yorodumi- PDB-8rdp: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
+Open data
-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 | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / CEREBLON / Ubiquitination / E3 / MOLECULAR GLUE / spiro-isoxazole | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / : / PHOSPHATE ION / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 Å | ||||||
Authors | Bischof, L. / Hartmann, M.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rdp.cif.gz | 142.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rdp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/8rdp ftp://data.pdbj.org/pub/pdb/validation_reports/rd/8rdp | HTTPS FTP |
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-Related structure data
Related structure data | 8rdqC 8rdrC 8rdsC 8rdtC C: citing same article (ref.) |
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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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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.) Magnetospirillum gryphiswaldense (magnetotactic) Gene: MGR_0879 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4TVL0 |
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-Non-polymers , 5 types, 96 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0001 Å | ||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→47.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.071 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.124 / 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: 1.2 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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