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- PDB-4b9k: pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b9k | ||||||
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Title | pVHL-ELOB-ELOC complex_(2S,4R)-1-(3-amino-2-methylbenzoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide bound | ||||||
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![]() | LIGASE / INHIBITOR | ||||||
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 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 / cellular response to hypoxia / regulation of gene expression / Neddylation / protein-macromolecule adaptor activity / Replication of the SARS-CoV-2 genome / DNA-binding transcription factor binding / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / 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 | ![]() ![]() ![]() | ||||||
![]() | Buckley, D.L. / Gustafson, J.L. / VanMolle, I. / Roth, A.G. / SeopTae, H. / Gareiss, P.C. / Jorgensen, W.L. / Ciulli, A. / Crews, C.M. | ||||||
![]() | ![]() Title: Small-Molecule Inhibitors of the Interaction between the E3 Ligase Vhl and Hif1 Alpha Authors: Buckley, D.L. / Gustafson, J.L. / Van Molle, I. / Roth, A.G. / Tae, H.S. / Gareiss, P.C. / Jorgensen, W.L. / Ciulli, A. / Crews, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 563.3 KB | Display | ![]() |
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PDB format | ![]() | 465.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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 on special symmetry positions |
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Components
-TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 3 types, 8 molecules ADGJBHKE
#1: Protein | Mass: 11956.372 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 10974.616 Da / Num. of mol.: 3 / Fragment: RESIDUES 17-112 Source method: isolated from a genetically manipulated source Details: CYS 112 HAS NOT BEEN OBSERVED AS MODIFIED TO CAS / Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | | Mass: 11078.599 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-112 Source method: isolated from a genetically manipulated source Details: CYS 112 HAS BEEN MODIFIED TO CAS BY PRESENCE OF ARSENIC ACID AND DTT IN THE CRYSTALLIZATION BUFFER Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 1 types, 4 molecules CFIL
#3: Protein | Mass: 19906.479 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 905 molecules ![](data/chem/img/TG0.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
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#5: Chemical | ChemComp-TG0 / ( #6: Chemical | ChemComp-ACT / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | GS AT N-TERMINUS LEFT AFTER CLEAVING OFF HIS-TAG ADDITIONAL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA CACODYLATE, PH 6.0, 0.2 M MG ACTETATE, 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: Jun 16, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 108859 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Biso Wilson estimate: 34.99 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.15 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.61 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: APO STRUCTURE V54BC Resolution: 2→46.06 Å / Cor.coef. Fo:Fc: 0.9492 / Cor.coef. Fo:Fc free: 0.9356 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.144 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11572. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=120. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11572. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=120. NUMBER TREATED BY BAD NON-BONDED CONTACTS=15.
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Displacement parameters | Biso mean: 43.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 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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