MolNFT v1 · #38003 · protein
Distinct functional domains of UBC9 dictate cell survival and resistance to genotoxic stress
2GJD · Ubiquitin-conjugating enzyme E2-18 kda: “Distinct functional domains of UBC9 dictate cell survival and resistance to genotoxic stress”. X-ray diffraction, 4 pockets (best druggability 0.78). MolNFT v1 #38003 on GenesisL1: 3D…
- 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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