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- PDB-8bb4: Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bb4 | ||||||
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Title | Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker | ||||||
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Function / homology | ![]() regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / MLL3/4 complex / elongin complex / Set1C/COMPASS complex / MLL1/2 complex / VCB complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / MLL3/4 complex / elongin complex / Set1C/COMPASS complex / MLL1/2 complex / VCB complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kraemer, A. / Doelle, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization. Authors: Schwalm, M.P. / Kramer, A. / Dolle, A. / Weckesser, J. / Yu, X. / Jin, J. / Saxena, K. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.5 KB | Display | ![]() |
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PDB format | ![]() | 211.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7q2jSC ![]() 8bb5C ![]() 8c13C S: Starting model for refinement 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
-Protein , 4 types, 4 molecules IOPQ
#1: Protein | Mass: 11748.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11043.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 18702.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 35296.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 2 types, 59 molecules ![](data/chem/img/Q3R.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-Q3R / ~{ |
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#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: 2.63 Å3/Da / Density % sol: 53.2 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 21-28% PEG 3350 0.4 M KSCN 0.1 M HEPES pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 10, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→184.51 Å / Num. obs: 19494 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.105 / Rrim(I) all: 0.149 / Net I/σ(I): 6 / Num. measured all: 38524 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.416
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7Q2J Resolution: 2.8→92.25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.863 / SU B: 43.624 / SU ML: 0.388 / SU R Cruickshank DPI: 0.3222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 111.62 Å2 / Biso mean: 48.286 Å2 / Biso min: 7.31 Å2
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Refinement step | Cycle: final / Resolution: 2.8→92.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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