[English] 日本語
Yorodumi- PDB-8jvd: Identification of small-molecule binding sites of a ubiquitin-con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jvd | ||||||
---|---|---|---|---|---|---|---|
Title | Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening | ||||||
Components | Ubiquitin-conjugating enzyme E2 T | ||||||
Keywords | LIGASE / UBE2T / ubiquitination / fragment-based drug discovery | ||||||
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: 1.696 Å | ||||||
Authors | Anantharajan, J. / Baburajendran, N. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Protein Sci. / Year: 2024 Title: Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening. Authors: Loh, Y.Y. / Anantharajan, J. / Huang, Q. / Xu, W. / Fulwood, J. / Ng, H.Q. / Ng, E.Y. / Gea, C.Y. / Choong, M.L. / Tan, Q.W. / Koh, X. / Lim, W.H. / Nacro, K. / Cherian, J. / Baburajendran, ...Authors: Loh, Y.Y. / Anantharajan, J. / Huang, Q. / Xu, W. / Fulwood, J. / Ng, H.Q. / Ng, E.Y. / Gea, C.Y. / Choong, M.L. / Tan, Q.W. / Koh, X. / Lim, W.H. / Nacro, K. / Cherian, J. / Baburajendran, N. / Ke, Z. / Kang, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jvd.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jvd.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 8jvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jvd_validation.pdf.gz | 779.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jvd_full_validation.pdf.gz | 780.2 KB | Display | |
Data in XML | 8jvd_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 8jvd_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/8jvd ftp://data.pdbj.org/pub/pdb/validation_reports/jv/8jvd | HTTPS FTP |
-Related structure data
Related structure data | 8jucC 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-V2R / Mass: 152.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5FN2O / Feature type: SUBJECT OF INVESTIGATION |
#3: 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: 3.82 Å3/Da / Density % sol: 67.83 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.5M 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: 0.95373 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→46.891 Å / Num. obs: 31816 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.011 / Rrim(I) all: 0.057 / Χ2: 0.53 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 96.2 % / Redundancy: 24.5 % / Rmerge(I) obs: 1.461 / Num. measured all: 38385 / Num. unique obs: 1569 / CC1/2: 0.916 / Rpim(I) all: 0.296 / Rrim(I) all: 0.01492 / Χ2: 0.43 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.696→46.891 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.76 / 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: 1.696→46.891 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|