Research workbench
Distinct functional domains of UBC9 dictate cell survival and resistance to genotoxic stress
Analyse Distinct functional domains of UBC9 dictate cell survival and resistance to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GJD
- Type
- protein
- Length
- 621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2-18 kda
- EC
- 6.3.2.19
- UniProt
- P50623
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Ubiquitin-conjugating enzyme E2-18 kda (EC 6.3.2.19) | protein | 155 | 34% helix, 21% strand | P50623 |
| B | Ubiquitin-conjugating enzyme E2-18 kda (EC 6.3.2.19) | protein | 156 | 35% helix, 21% strand | P50623 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.78 | 0.81 | 68 | empty |
| 2 | 752 | 0.73 | 0.78 | 58 | empty |
| 3 | 616 | 0.72 | 0.79 | 61 | empty |
| 4 | 72 | 0.42 | 0.80 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 706 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 407 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 335 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 299 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 131 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GJD · Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic… · the same entry in another collection · chain A against A, TM-score 1.00
- P50623 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P50623) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P50623
- Elsewhere: RCSB PDB 2GJD · PDBe 2GJD · UniProt P50623
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