[English] 日本語
Yorodumi- PDB-8jvl: Identification and characterization of inhibitors covalently modi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jvl | ||||||
---|---|---|---|---|---|---|---|
Title | Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer | ||||||
Components | Ubiquitin-conjugating enzyme E2 T | ||||||
Keywords | LIGASE/INHIBITOR / UBE2T / structure / drug discovery / covalent inhibitor / Fanconi anemia / LIGASE-inhibitor complex | ||||||
Function / homology | Function and homology information protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Fanconi Anemia Pathway / protein polyubiquitination / ubiquitin-protein transferase activity / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin binding / nucleolus / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Anantharajan, J. / Baburajendran, N. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer. Authors: Anantharajan, J. / Tan, Q.W. / Fulwood, J. / Sifang, W. / Huang, Q. / Ng, H.Q. / Koh, X. / Xu, W. / Cherian, J. / Baburajendran, N. / Kang, C. / Ke, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jvl.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jvl.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 8jvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jvl_validation.pdf.gz | 676.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jvl_full_validation.pdf.gz | 676.8 KB | Display | |
Data in XML | 8jvl_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 8jvl_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/8jvl ftp://data.pdbj.org/pub/pdb/validation_reports/jv/8jvl | HTTPS FTP |
-Related structure data
Related structure data | 8jveC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17830.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2T / Production host: Escherichia coli (E. coli) References: UniProt: Q9NPD8, E2 ubiquitin-conjugating enzyme |
---|---|
#2: Chemical | ChemComp-V5L / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.8 M Sodium formate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95365 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→47.14 Å / Num. obs: 18267 / % possible obs: 99.6 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.017 / Rpim(I) all: 0.028 / Rrim(I) all: 0.144 / Χ2: 0.54 / Net I/σ(I): 15.6 / Num. measured all: 467470 |
Reflection shell | Resolution: 2.06→2.12 Å / % possible obs: 94.8 % / Redundancy: 24.4 % / Rmerge(I) obs: 2.05 / Num. measured all: 32302 / Num. unique obs: 1322 / CC1/2: 0.871 / Rpim(I) all: 0.409 / Rrim(I) all: 0.02092 / Χ2: 0.46 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→47.14 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→47.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|