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- PDB-6r1c: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r1c | ||||||
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Title | Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a | ||||||
![]() | Cereblon isoform 4 | ||||||
![]() | SIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / ASPARTIC ACID / S-Thalidomide / Chem-JOW / PHOSPHATE ION / Cereblon isoform 4![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heim, C. / Hartmann, M.D. | ||||||
![]() | ![]() Title: De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives. Authors: Heim, C. / Pliatsika, D. / Mousavizadeh, F. / Bar, K. / Hernandez Alvarez, B. / Giannis, A. / 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 | ![]() | 156.1 KB | Display | ![]() |
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PDB format | ![]() | 122.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6r0qC ![]() 6r0sC ![]() 6r0uC ![]() 6r0vC ![]() 6r11C ![]() 6r12C ![]() 6r13C ![]() 6r18C ![]() 6r19C ![]() 6r1aC ![]() 6r1dC ![]() 6r1kC ![]() 6r1wC ![]() 6r1xC ![]() 4v2yS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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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 , 7 types, 233 molecules ![](data/chem/img/ASP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EF2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/JOW.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EF2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/JOW.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ASP / | ||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-JOW / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.4 M Ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→49.12 Å / Num. obs: 48555 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.29 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 7572 / CC1/2: 0.87 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4v2y Resolution: 1.5→49.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.253 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.005 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→49.12 Å
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Refine LS restraints |
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