+Open data
-Basic information
Entry | Database: PDB / ID: 2kre | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of E4B/UFD2A U-Box domain | ||||||
Components | Ubiquitin conjugation factor E4 B | ||||||
Keywords | PROTEIN BINDING / U-BOX DOMAIN / E3 UBIQUITIN LIGASE / E4 POLYUBIQUITIN CHAIN ELONGATION FACTOR / Phosphoprotein / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / ubiquitin ligase complex / : / response to UV / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding ...granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / ubiquitin ligase complex / : / response to UV / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Nomine, Y. / Wasielewski, E. / Botuyan, M. / Mer, G. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4. Authors: Benirschke, R.C. / Thompson, J.R. / Nomine, Y. / Wasielewski, E. / Juranic, N. / Macura, S. / Hatakeyama, S. / Nakayama, K.I. / Botuyan, M.V. / Mer, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2kre.cif.gz | 631.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2kre.ent.gz | 522.2 KB | Display | PDB format |
PDBx/mmJSON format | 2kre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/2kre ftp://data.pdbj.org/pub/pdb/validation_reports/kr/2kre | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 11548.991 Da / Num. of mol.: 1 / Fragment: UNP residues 1208-1302 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDNB1, KIAA0684, UBE4B, UFD2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95155 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sample conditions | Ionic strength: 50 mM NACL / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |