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Yorodumi- PDB-5nvw: pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarb... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5nvw | ||||||
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| Title | pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) | ||||||
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Keywords | LIGASE / protein complex / ubiquitin ligase / hypoxia inducible factor | ||||||
| Function / homology | Function and homology informationregulation 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 / Replication of the SARS-CoV-1 genome / VCB complex / 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 / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / 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 / protein serine/threonine kinase binding / transcription corepressor binding / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / 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 / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
| Model details | pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4- ...pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-(cyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 6) | ||||||
Authors | Gadd, M.S. / Soares, P. / Galdeano, C. / Ciulli, A. | ||||||
| Funding support | 1items
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Citation | Journal: J. Med. Chem. / Year: 2018Title: Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)- ...Title: Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298). Authors: Soares, P. / Gadd, M.S. / Frost, J. / Galdeano, C. / Ellis, L. / Epemolu, O. / Rocha, S. / Read, K.D. / Ciulli, A. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5nvw.cif.gz | 564.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5nvw.ent.gz | 465 KB | Display | PDB format |
| PDBx/mmJSON format | 5nvw.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5nvw_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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| Full document | 5nvw_full_validation.pdf.gz | 1.4 MB | Display | |
| Data in XML | 5nvw_validation.xml.gz | 56.4 KB | Display | |
| Data in CIF | 5nvw_validation.cif.gz | 82.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/5nvw ftp://data.pdbj.org/pub/pdb/validation_reports/nv/5nvw | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5nvvC ![]() 5nvxC ![]() 5nvyC ![]() 5nvzC ![]() 5nw0C ![]() 5nw1C ![]() 5nw2C ![]() 1vcbS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
| #1: Protein | Mass: 11956.372 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Plasmid: pCDFDuet-1 / Production host: ![]() #2: Protein | Mass: 10974.616 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Plasmid: pCDFDuet-1 / Production host: ![]() #3: Protein | Mass: 18806.273 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Plasmid: pHAT4 / Production host: ![]() #4: Chemical | ChemComp-9BW / ( #5: Water | ChemComp-HOH / | Has protein modification | 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: 2.44 Å3/Da / Density % sol: 49.55 % / Mosaicity: 0.04 ° |
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| Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG 3350, MgOAc, Sodium cacodylate, DTT |
-Data collection
| Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å | |||||||||||||||||||||
| Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2014 | |||||||||||||||||||||
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
| Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 | |||||||||||||||||||||
| Reflection | Resolution: 2.2→48.93 Å / Num. obs: 82957 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.058 / Rrim(I) all: 0.153 / Net I/σ(I): 8.6 | |||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1VCB Resolution: 2.2→48.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.968 / SU ML: 0.164 / SU R Cruickshank DPI: 0.2718 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.215 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso max: 120.73 Å2 / Biso mean: 36.545 Å2 / Biso min: 12.74 Å2
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| Refinement step | Cycle: final / Resolution: 2.2→48.93 Å
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| Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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