+Open data
-Basic information
Entry | Database: PDB / ID: 7u3k | ||||||
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Title | GID4 in complex with compound 89 | ||||||
Components | Glucose-induced degradation protein 4 homolog | ||||||
Keywords | PEPTIDE BINDING PROTEIN/INHIBITOR / Complex / Inhibitor / Protein degradation / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / Regulation of pyruvate metabolism / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Chem-L73 / Glucose-induced degradation protein 4 homolog Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.198 Å | ||||||
Authors | Chana, C.K. / Sicheri, F. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4. Authors: Chana, C.K. / Maisonneuve, P. / Posternak, G. / Grinberg, N.G.A. / Poirson, J. / Ona, S.M. / Ceccarelli, D.F. / Mader, P. / St-Cyr, D.J. / Pau, V. / Kurinov, I. / Tang, X. / Deng, D. / Cui, ...Authors: Chana, C.K. / Maisonneuve, P. / Posternak, G. / Grinberg, N.G.A. / Poirson, J. / Ona, S.M. / Ceccarelli, D.F. / Mader, P. / St-Cyr, D.J. / Pau, V. / Kurinov, I. / Tang, X. / Deng, D. / Cui, W. / Su, W. / Kuai, L. / Soll, R. / Tyers, M. / Rost, H.L. / Batey, R.A. / Taipale, M. / Gingras, A.C. / Sicheri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u3k.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u3k.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 7u3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u3k_validation.pdf.gz | 783.6 KB | Display | wwPDB validaton report |
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Full document | 7u3k_full_validation.pdf.gz | 785.1 KB | Display | |
Data in XML | 7u3k_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 7u3k_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/7u3k ftp://data.pdbj.org/pub/pdb/validation_reports/u3/7u3k | HTTPS FTP |
-Related structure data
Related structure data | 7u3eC 7u3fC 7u3gC 7u3hC 7u3iC 7u3jC 7u3lC 6ccrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19604.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Plasmid: PET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IVV7 | ||||
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#2: Chemical | ChemComp-L73 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG6000, 0.1 M HEPES, 0.2 M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 9, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.198→39.279 Å / Num. obs: 9021 / % possible obs: 98.8 % / Redundancy: 9.63 % / Biso Wilson estimate: 63.139 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.129 / Χ2: 0.757 / Net I/σ(I): 9.55 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CCR Resolution: 2.198→39.279 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.31 Å2 / Biso mean: 71.5762 Å2 / Biso min: 40.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.198→39.279 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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