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- PDB-8ood: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -
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Open data
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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 | ||||||
![]() | DDB1- and CUL4-associated factor 1 | ||||||
![]() | TRANSFERASE / DCAF1 / Ligase / compound | ||||||
Function / homology | ![]() 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 / post-translational protein modification / B cell differentiation / 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 / post-translational protein modification / B cell differentiation / 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 / protein serine kinase activity / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schroeder, M. / Renatus, M. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.5 KB | Display | ![]() |
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PDB format | ![]() | 195.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8oo5C 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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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.) ![]() ![]() ![]() References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 326 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/VY3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/VY3.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |