MolNFT v1 · #74123 · protein
Crystal structure of UBA2UFD-UBC9: insights into E1-E2 interactions in sumo pathways
3ONG · Ubiquitin-activating enzyme E1-like: “Crystal structure of UBA2UFD-UBC9: insights into E1-E2 interactions in sumo pathways”. X-ray diffraction, 3 pockets (best druggability 0.62). MolNFT v1 #74123 on GenesisL1: 3D structure, binding…
- PDB
- 3ONG
- Type
- protein
- Length
- 542 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1-like; Sumo-conjugating enzyme UBC9
- EC
- 6.3.2.-
- UniProt
- P52488, P50623
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1-like | protein | 114 | 18% helix, 36% strand | P52488 |
| B | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 158 | 35% helix, 20% strand | P50623 |
| C | Ubiquitin-activating enzyme E1-like | protein | 113 | 17% helix, 34% strand | P52488 |
| D | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 157 | 34% helix, 19% strand | P50623 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.62 | 0.76 | 52 | empty |
| 2 | 182 | 0.50 | 0.77 | 26 | empty |
| 3 | 113 | 0.49 | 0.80 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 890 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 339 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3ONG · Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways · the same entry in another collection · chain D against D, TM-score 1.00
- P52488 · AlphaFold monomer V2.0 prediction for ubiquitin-activating enzyme E1-like (P52488) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P50623 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P50623) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P52488
- Every structure of UniProt P50623
- Elsewhere: RCSB PDB 3ONG · PDBe 3ONG · UniProt P52488 · UniProt P50623
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