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Yorodumi- PDB-8ood: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ood | ||||||
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Title | Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15 | ||||||
Components | DDB1- and CUL4-associated factor 1 | ||||||
Keywords | TRANSFERASE / DCAF1 / Ligase / compound | ||||||
Function / homology | Function and homology information histone H2AT120 kinase activity / cell competition in a multicellular organism / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process ...histone H2AT120 kinase activity / cell competition in a multicellular organism / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / non-specific serine/threonine protein kinase / protein ubiquitination / phosphorylation / protein serine kinase activity / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å | ||||||
Authors | Schroeder, M. / Renatus, M. | ||||||
Funding support | 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings Authors: Schroder, M. / Renatus, M. / Thoma, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ood.cif.gz | 249.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ood.ent.gz | 195.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ood.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ood_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ood_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8ood_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 8ood_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/8ood ftp://data.pdbj.org/pub/pdb/validation_reports/oo/8ood | HTTPS FTP |
-Related structure data
Related structure data | 8oo5C 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41764.824 Da / Num. of mol.: 1 / Mutation: Q1250L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 326 molecules
#2: Chemical | ChemComp-MG / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.13M LiSO4, 0.1M Tris pH 7.5 |
-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 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.497→52.259 Å / Num. obs: 74179 / % possible obs: 99.6 % / Redundancy: 8.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.033 / Rrim(I) all: 0.097 / Χ2: 0.86 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.5→1.52 Å / % possible obs: 94 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.726 / Num. measured all: 26759 / Num. unique obs: 3405 / CC1/2: 0.452 / Rpim(I) all: 0.652 / Rrim(I) all: 1.852 / Χ2: 0.79 / Net I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.497→52.259 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.23 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.059 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.866 Å2
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Refinement step | Cycle: LAST / Resolution: 1.497→52.259 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -14.9699 Å / Origin y: -31.6907 Å / Origin z: 11.4333 Å
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Refinement TLS group | Selection: ALL |