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Open data
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Basic information
Entry | Database: PDB / ID: 6gmx | ||||||||||||||||||
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Title | pVHL:EloB:EloC in complex with 6-chlorothiochroman-4-one | ||||||||||||||||||
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![]() | ONCOPROTEIN / E3 ubiquitin ligase / tumor supressor / PROTAC / fragment-based drug discovery | ||||||||||||||||||
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 / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase 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 / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / Neddylation / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Van Molle, I. / Lucas, X. / Ciulli, A. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. Authors: Lucas, X. / Van Molle, I. / Ciulli, A. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 539 KB | Display | ![]() |
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PDB format | ![]() | 454.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 559.3 KB | Display | ![]() |
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Full document | ![]() | 577 KB | Display | |
Data in XML | ![]() | 53 KB | Display | |
Data in CIF | ![]() | 73.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 5 types, 12 molecules AGJBHKCFILDE
#1: Protein | Mass: 11956.372 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: S-(DIMETHYLARSENIC)CYSTEINE modification / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 10974.616 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: 2nd N at N-treminus resulting from cloning / Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 18806.273 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: residues 54-213 GS at N-terminus from cloning S-(DIMETHYLARSENIC)CYSTEINE modification Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | | Mass: 11852.390 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: S-(DIMETHYLARSENIC)CYSTEINE modification / Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | | Mass: 11078.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 2nd N at N-treminus resulting from cloning / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 363 molecules ![](data/chem/img/F7B.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-IPA / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→94 Å / Num. obs: 67228 / % possible obs: 99.5 % / Redundancy: 12.7 % / Biso Wilson estimate: 48.55 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.24 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.37→2.52 Å / Mean I/σ(I) obs: 2.2 / CC1/2: 0.828 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.533→94 Å
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