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Yorodumi- PDB-4bks: von Hippel Lindau protein:ElonginB:ElonginC complex, in complex w... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4bks | ||||||
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| Title | von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-1-ethanoyl-N-[[4-(1,3-oxazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / E3 UBIQUITIN LIGASE / FRAGMENT BASED DRUG DISCOVERY | ||||||
| Function / homology | Function and homology informationregulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / 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 / 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 / protein serine/threonine kinase binding / negative regulation of autophagy / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / 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 / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / cilium / 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 / 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 / OTHER / Resolution: 2.2 Å | ||||||
Authors | Van Molle, I. / Dias, D.M. / Baud, M. / Galdeano, C. / Geraldes, C.F.G.C. / Ciulli, A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2014Title: Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions? Authors: Dias, D.M. / Van Molle, I. / Baud, M.G.J. / Galdeano, C. / Geraldes, C.F.G.C. / 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 | 4bks.cif.gz | 550.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4bks.ent.gz | 455 KB | Display | PDB format |
| PDBx/mmJSON format | 4bks.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4bks_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 4bks_full_validation.pdf.gz | 1.5 MB | Display | |
| Data in XML | 4bks_validation.xml.gz | 63.2 KB | Display | |
| Data in CIF | 4bks_validation.cif.gz | 83.1 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bks ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bks | 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
-TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 3 types, 8 molecules AJBEHKDG
| #1: Protein | Mass: 11852.389 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF_DUET1 / Production host: ![]() #2: Protein | Mass: 10974.616 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-96 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF_DUET1 / Production host: ![]() #4: Protein | Mass: 11748.406 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDF_DUET1 / Production host: ![]() |
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-Protein , 1 types, 4 molecules CFIL
| #3: Protein | Mass: 18806.273 Da / Num. of mol.: 4 / Fragment: RESIDUES 214-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHAT4 / Production host: ![]() |
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-Non-polymers , 3 types, 610 molecules 




| #5: Chemical | ChemComp-X6C / ( #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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| Nonpolymer details | O74: THE LIGAND 6-(4-(2-CHLOROANILINO)-1H-QUINAZOLIN-2-YLIDENE) CYCLOHEXA-2, 4-DIEN-1-ONE IS BOUND ...O74: THE LIGAND 6-(4-(2-CHLOROANIL |
| Sequence details | GS LEFT FROM CLEAVABLE TAG 2 MET AT N-TERMINUS DUE TO CLONING |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % / Description: NONE |
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| Crystal grow | Details: 0.1M NA CACODYALATE PH 6.0, 0.2M MG ACETATE, 15%PEG3350, 5MM DTT |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2012 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
| Reflection | Resolution: 2.2→50 Å / Num. obs: 83354 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 12.9 % / Biso Wilson estimate: 46.23 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.95 |
| Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.18 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.2→45.47 Å / Cor.coef. Fo:Fc: 0.9529 / Cor.coef. Fo:Fc free: 0.9396 / SU R Cruickshank DPI: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.231 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.181 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11117. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=48. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11117. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=48. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
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| Displacement parameters | Biso mean: 57.69 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.2→45.47 Å
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| LS refinement shell | Resolution: 2.2→2.26 Å / 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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HOMO SAPIENS (human)
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