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Yorodumi- PDB-4bks: von Hippel Lindau protein:ElonginB:ElonginC complex, in complex w... -
+Open data
-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 information 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 initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-macromolecule adaptor activity / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / 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: 2014 Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bks.cif.gz | 545.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bks.ent.gz | 465.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bks ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bks | HTTPS FTP |
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-Related structure data
-Links
-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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370 #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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369 #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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15370 |
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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: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337 |
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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
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 |
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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 |
-Processing
Software |
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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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Refine LS restraints |
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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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